Optimized non-canonical zinc finger proteins

ABSTRACT

Disclosed herein are zinc fingers comprising CCHC zinc coordinating residues. Also described are zinc finger proteins and fusion proteins comprising these CCHC zinc fingers as well as polynucleotides encoding these proteins. Methods of using these proteins for gene editing and gene regulation are also described.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims the benefit of U.S. ProvisionalApplication No. 60/874,911, filed Dec. 14, 2006 and U.S. ProvisionalApplication No. 60/932,497 filed May 30, 2007, both of which disclosuresare hereby incorporated by reference in their entireties herein.

TECHNICAL FIELD

The present disclosure is in the fields of genome engineering, genetargeting, targeted chromosomal integration, protein expression andepigenome editing.

BACKGROUND

Sequence-specific binding of proteins to DNA, RNA, protein and othermolecules is involved in a number of cellular processes such as, forexample, transcription, replication, chromatin structure, recombination,DNA repair, RNA processing and translation. The binding specificity ofcellular binding proteins that participate in protein-DNA, protein-RNAand protein-protein interactions contributes to development,differentiation and homeostasis.

Zinc finger proteins (ZFPs) are proteins that can bind to DNA in asequence-specific manner. Zinc fingers were first identified in thetranscription factor TFIIIA from the oocytes of the African clawed toad,Xenopus laevis. A single zinc finger domain of this class of ZFPs isabout 30 amino acids in length, and several structural studies havedemonstrated that it contains a beta turn (containing two conservedcysteine residues) and an alpha helix (containing two conservedhistidine residues), which are held in a particular conformation throughcoordination of a zinc atom by the two cysteines and the two histidines.This class of ZFPs is also known as C2H2 ZFPs. Additional classes ofZFPs have also been suggested. See, e.g., Jiang et al. (1996) J. Biol.Chem. 271:10723-10730 for a discussion of Cys-Cys-His-Cys (C3H) ZFPs. Todate, over 10,000 zinc finger sequences have been identified in severalthousand known or putative transcription factors. Zinc finger domainsare involved not only in DNA recognition, but also in RNA binding and inprotein-protein binding. Current estimates are that this class ofmolecules will constitute about 2% of all human genes.

Most zinc finger proteins have conserved cysteine and histidine residuesthat tetrahedrally-coordinate the single zinc atom in each fingerdomain. In particular, most ZFPs are characterized by finger componentsof the general sequence:-Cys-(X)₂₋₄-Cys-(X)₁₂-His-(X)₃₋₅-His- (SEQ IDNO: 1), in which X represents any amino acid (the C₂H₂ ZFPs). Thezinc-coordinating sequences of this most widely represented classcontain two cysteines and two histidines with particular spacings. Thefolded structure of each finger contains an antiparallel β-turn, afinger tip region and a short amphipathic α-helix. The metalcoordinating ligands bind to the zinc ion and, in the case ofzif268-type zinc fingers, the short amphipathic α-helix binds in themajor groove of DNA. In addition, the structure of the zinc finger isstabilized by certain conserved hydrophobic amino acid residues (e.g.,the residue directly preceding the first conserved Cys and the residueat position +4 of the helical segment of the finger) and by zinccoordination through the conserved cysteine and histidine residues.

Canonical (C2H2) zinc finger proteins having alterations in positionsmaking direct base contacts, ‘supporting’ or ‘buttressing’ residuesimmediately adjacent to the base-contacting positions, and positionscapable of contacting the phosphate backbone of the DNA have beendescribed. See, e.g., U.S. Pat. Nos. 6,007,988; 6,013,453; 6,140,081;6,866,997; 6,746,838; 6,140,081; 6,610,512; 7,101,972; 6,453,242;6,785,613; 7,013,219; PCT WO 98/53059; Choo et al. (2000) Curr. Opin.Struct. Biol. 10:411-416; Segal et al. (2000) Curr. Opin. Chem. Biol.4:34-39.

In addition, zinc finger proteins containing zinc fingers with modifiedzinc coordinating residues have also been described (see, e.g., U.S.Patent Application Nos. 20030108880, 20060246567 and 20060246588; thedisclosures of which are incorporated by reference). However, while zincfinger proteins containing these non-canonical zinc fingers retain genetranscription regulatory function, their ability to act as zinc fingernucleases (ZFNs) is in some cases diminished relative to zinc fingerproteins consisting exclusively of canonical, C2H2 zinc fingers.

Thus, there remains a need, particularly in the construction of zincfinger nucleases, for additional engineered zinc finger binding proteinscontaining zinc fingers having optimized non-canonical zinc coordinatingregions.

SUMMARY

The present disclosure provides zinc finger DNA-binding domains withalterations in at least one zinc coordinating residue. In particular,described herein are CCHC zinc fingers. These CCHC zinc fingers canfurther comprise additional alterations (substitutions, insertionsand/or deletions), in the vicinity of the zinc coordinating residues,for example in the residues surrounding the C-terminal-most zinccoordinating residue of the zinc finger. Zinc finger polypeptides andfusion proteins comprising one or more these CCHC zinc fingers,polynucleotides encoding these zinc fingers and fusion proteins andmethods of using these zinc finger polypeptides and/or fusion proteinsare also described.

Thus, the present disclosure encompasses, but is not limited to, thefollowing numbered embodiments:

1. A zinc finger protein comprising a non-canonical (non-C₂H₂) zincfinger, wherein the non-canonical zinc finger has a helical portioninvolved in DNA binding and wherein the zinc-coordinating region of thehelical portion comprises the amino acid sequence HX₁X₂RCX_(L) (SEQ IDNO:2); and wherein the zinc finger protein is engineered to bind to atarget sequence.

2. The zinc finger protein of embodiment 1, wherein X₁ is A and X₂ is Q.

3. The zinc finger protein of embodiment 1, wherein X₁ is K and X₂ is E.

4. The zinc finger protein of embodiment 1, wherein X₁ is T and X₂ is R.

5. The zinc finger protein of embodiment 1, wherein X_(L) is G.

6. A zinc finger protein comprising two or more zinc fingers, wherein atleast one zinc finger comprises the sequenceCys-(X^(A))₂₋₄-Cys-(X^(B))₁₂-His-(X^(C))₃₋₅-Cys-(X^(D))₁₋₁₀ (SEQ IDNO:3), where X^(A), X^(B), X^(C) and X^(D) can be any amino acid.

7. The zinc finger protein of any of embodiments 1 to 6, comprising anyof the sequences shown in any of Tables 1, 2, 3 or 4.

8. The zinc finger protein of any of embodiments 6 or 7, wherein X^(D)comprises the sequence QLV or QKP.

9. The zinc finger protein of embodiment 8, wherein the sequence QLV orQKP are the 3 C-terminal amino acid residues of the zinc finger.

10. The zinc finger protein of any of embodiments 6 to 9, wherein X^(D)comprises 1, 2 or 3 Gly (G) residues.

11. A zinc finger protein comprising a plurality of zinc fingers,wherein at least one of the zinc fingers comprises a CCHC zinc fingeraccording to any of embodiments 1 to 10.

12. The zinc finger protein of embodiment 11, wherein the zinc fingerprotein comprises 3, 4, 5 or 6 zinc fingers.

13. The zinc finger protein of embodiment 11 or 12, wherein finger 2comprises the CCHC zinc finger.

14. The zinc finger protein of any of embodiments 11 to 13, wherein theC-terminal zinc finger comprises the CCHC finger.

15. The zinc finger protein of any of embodiments 11 to 14, wherein atleast two zinc fingers comprise the CCHC zinc finger.

16. The zinc finger protein of any of embodiments 11 to 15, wherein thezinc finger protein comprises any of the sequences shown in Table 8 andis engineered to bind to a target sequence in an IPP2-K gene.

17. A fusion protein comprising a zinc finger protein of any ofembodiments 1 to 16 and one or more functional domains.

18. A fusion protein comprising:

(a) a cleavage half-domain,

(b) the zinc finger protein of any of embodiments 1 to 16, and

(c) a ZC linker interposed between the cleavage half-domain and the zincfinger protein.

19. The fusion protein of embodiment 18, wherein the length of the ZClinker is 5 amino acids.

20. The fusion protein of embodiment 19, wherein the amino acid sequenceof the ZC linker is GLRGS (SEQ ID NO:4).

21. The fusion protein of embodiment 18, wherein the length of the ZClinker is 6 amino acids.

22. The fusion protein of embodiment 21, wherein the amino acid sequenceof the ZC linker is GGLRGS (SEQ ID NO:5).

23. A polynucleotide encoding a zinc finger protein according to any ofembodiments 1 to 16 or a fusion protein according to any of embodiments17 to 22.

24. A method for targeted cleavage of cellular chromatin in a plantcell, the method comprising expressing, in the cell, a pair of fusionproteins according to any of embodiments 18 to 22; wherein:

(a) the target sequences of the fusion proteins are within tennucleotides of each other; and

(b) the fusion proteins dimerize and cleave DNA located between thetarget sequences.

25. A method of targeted genetic recombination in a host plant cell, themethod comprising:

(a) expressing, in the host cell, a pair of fusion proteins according toany of embodiments 18 to 22, wherein the target sequences of the fusionproteins are present in a chosen host target locus; and

(b) identifying a recombinant host cell which exhibits a sequencealteration in the host target locus.

26. The method of either of embodiment 24 or 25, wherein the sequencealteration is a mutation selected from the group consisting of adeletion of genetic material, an insertion of genetic material, asubstitution of genetic material and any combination thereof.

27. The method of any of embodiments 24 to 26, further comprisingintroducing an exogenous polynucleotide into the host cell.

28. The method of embodiment 27, wherein the exogenous polynucleotidecomprises sequences homologous to the host target locus.

29. The method of any of embodiments 24 to 28, wherein the plant isselected from the group consisting of a monocotyledon, a dicotyledon,gymnosperms and eukaryotic algae.

30. The method of embodiment 29, wherein the plant is selected from thegroup consisting of maize, rice, wheat, potato, soybean, tomato,tobacco, members of the Brassica family, and Arabidopsis.

31. The method of any of embodiments 24 to 29 wherein the plant is atree.

32. The method of any of embodiments 24 to 31, wherein the targetsequences are in an IPP2K gene.

33. A method for reducing the level of phytic acid in seeds, the methodcomprising inactivating or altering an IPP2-K gene according toembodiment 32.

34. A method for making phosphorous more metabolically available inseed, the method comprising inactivating or altering an IPP2-K geneaccording to embodiment 32.

35. A plant cell comprising a zinc finger protein according to any ofembodiments 1 to 16, a fusion protein according to any of embodiments 17to 22 or a polynucleotide according to embodiment 23.

36. The plant cell of embodiment 35, wherein the cell is a seed.

37. The plant cell of embodiment 36, wherein seed is a corn seed.

38. The plant cell of any of embodiments 35 to 37, wherein IPP2-K ispartially or fully inactivated.

39. The plant cell of embodiment 38, wherein the levels of phytic acidin the seed are reduced.

40. The plant cell of embodiments 35 to 39, wherein metabolicallyavailable levels of phosphorous in the cell are increased.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a graph depicting gene correction rates, as measured by thepercentage of cells expressing GFP, in a GFP cell reporter assay systemas described in U.S. Patent No. 2005/0064474 and below. The ZFN variantsare designated “X-Y,” where “X” refers to the Table number and “Y”refers to the number given the zinc finger in the particularly selectedtable. For instance, “2-21” refers to a ZFN having a finger comprisingthe sequence shown in Table 2 in the row numbered 21, namelyHAQRCGLRGSQLV (SEQ ID NO:53).

FIG. 2 is a graph depicting percentage of Cel-1 signal resulting fromcleavage using various pairs of ZFN variants. The results of twoexperiments are shown for each pair of ZFNs by reference to samplenumber. The pairs of variants used for each sample are shown in the boxon the upper right corner, where “wt 5-8” and “wt 5-9” refer tocanonical ZFN pairs disclosed in Example 14 (Table 17) of U.S. PatentApplication No. 2005/0064474. In samples 3-12, the C-terminal region ofthe recognition helices of finger 2 or finger 4 of the canonical ZFN 5-8or 5-9 are replaced with non-canonical sequences. Partial sequence ofthe non-canonical ZFN variants designated 20, 21, 43, 45, 47 and 48 insamples 3-12 and the finger position of these variants within the4-fingered ZFN are shown in the top left corner above the graph. Theasterix above the bar depicting results from experiment 2 for samples 8and 9 indicates background in the lane, resulting in an underestimationof ZFN efficiency.

FIG. 3 is a graph depicting gene correction rates in the GFP cellreporter assay system described in U.S. Patent No. 2005/0064474 andherein. The ZFN pairs tested in each sample are shown below each bar,where the zinc finger numbers 20, 21, 43, 45, 47 and 48 are thosedescribed in Example 3 and CCHC zinc fingers 1a through 10a comprise thesequence shown in Tables 3 and 4. Zinc fingers 20, 21, 7a, 8a, 9a and10a were used in Finger 4; zinc fingers 43, 45, 47, 48, 1a, 2a, 3a, 4a,5a, and 6a were used in Finger 2.

FIG. 4 is a linear schematic representation of plasmid pDAB1585, atarget vector for tobacco.

FIG. 5 is a schematic representation of plasmid pDAB1585, a targetvector for tobacco.

FIGS. 6A and 6B depict zinc finger nucleases (ZFN). FIG. 6A is aschematic depicting ZFN binding. FIG. 6B shows the sequence of thetarget sequence.

FIG. 7 is a schematic representation of plasmid pDAB1400.

FIG. 8 is a schematic representation of plasmid pDAB782.

FIG. 9 is a schematic representation of plasmid pDAB1582.

FIG. 10 is a schematic representation of plasmid pDAB354.

FIG. 11 is a schematic representation of plasmid pDAB1583.

FIG. 12 is a schematic representation of plasmid pDAB2407.

FIG. 13 is a schematic representation of plasmid pDAB1584.

FIG. 14 is a schematic representation of plasmid pDAB2418.

FIG. 15 is a schematic representation of plasmid pDAB4045.

FIG. 16 is a schematic representation of plasmid pDAB1575.

FIG. 17 is a schematic representation of plasmid pDAB1577.

FIG. 18 is a schematic representation of plasmid pDAB1579.

FIG. 19 is a schematic representation of plasmid pDAB1580.

FIG. 20 is a schematic representation of plasmid pDAB3401.

FIG. 21 is a schematic representation of plasmid pDAB1570.

FIG. 22 is a schematic representation of plasmid pDAB1572.

FIG. 23 is a schematic representation of plasmid pDAB4003.

FIG. 24 is a schematic representation of plasmid pDAB1571.

FIG. 25 is a schematic representation of plasmid pDAB7204.

FIG. 26 is a schematic representation of plasmid pDAB1573.

FIG. 27 is a schematic representation of plasmid pDAB1574.

FIG. 28 is a schematic representation of plasmid pDAB1581.

FIG. 29 is a schematic representation of plasmid pDAB1576.

FIG. 30 are schematic representations of plasmid pDAB1600.

FIG. 31 is a schematic representation of plasmid pDAB3731.

FIG. 32 is a schematic representation of plasmid pDAB4322.

FIG. 33 is a schematic representation of plasmid pDAB4331.

FIG. 34 is a schematic representation of plasmid pDAB4332.

FIG. 35 is a schematic representation of plasmid pDAB4333.

FIG. 36 is a schematic representation of plasmid pDAB4334.

FIG. 37 is a schematic representation of plasmid pDAB4336.

FIG. 38 is a schematic representation of plasmid pDAB4339.

FIG. 39 is a schematic representation of plasmid pDAB4321.

FIG. 40 is a schematic representation of plasmid pDAB4323.

FIG. 41 is a schematic representation of plasmid pDAB4341.

FIG. 42 is a schematic representation of plasmid pDAB4342.

FIG. 43 is a schematic representation of plasmid pDAB4343.

FIG. 44 is a schematic representation of plasmid pDAB4344.

FIG. 45 is a schematic representation of plasmid pDAB4346.

FIG. 46 is a schematic representation of plasmid pDAB4330.

FIG. 47 is a schematic representation of plasmid pDAB4351.

FIG. 48 is a schematic representation of plasmid pDAB4356.

FIG. 49 is a schematic representation of plasmid pDAB4359.

FIG. 50 is a schematic representation of plasmid pDAB7002.

FIG. 51 is a schematic representation of plasmid pDAB7025.

FIG. 52 is a schematic representation of plasmid pDAB1591.

FIG. 53 is a schematic representation of plasmidpcDNA3.1-SCD27a-L0-FokI, the DNA template used for PCR amplification ofScd27 ZFN.

FIG. 54 is a schematic representation of plasmid pDAB1594.

FIG. 55 is a schematic representation of plasmid pDAB1598.

FIG. 56 is a schematic representation of plasmid pDAB1577.

FIG. 57 is a schematic representation of plasmid pDAB1578.

FIG. 58 is a schematic representation of plasmid pDAB1601, the PAT genecontrol vector.

FIG. 59 is a schematic depicting predicted intrachromosomal homologousrecombination stimulated by IL-1-Fok1 fusion protein.

FIG. 60 is a schematic representation of plasmid pDAB1590, a positiveGFP-expressing control.

FIG. 61 is a schematic depicting predicted inter-chromosomal homologousrecombination stimulated by IL-1 zinc finger-Fok1 fusion protein.

FIG. 62 is a schematic depicting predicted inter-chromosomal homologousrecombination stimulated by Scd27 Zinc Finger-Fok1 fusion protein.

FIG. 63 is a gel depicting PCR Analysis of the Recombinants. First 4lanes on the left are labeled above the gel. Lanes labeled 1-5 show HRevents from the transformation of BY2-380 with C3H IL-1-Fok1 fusionprotein gene and lanes labeled 6-7 show HR events from thetransformation of BY2-380 with C3H SCD27-Fok1 fusion protein gene.

FIG. 64 shows a maize IPP2K gene sequence (SEQ ID NO:6), derived fromHiII cell culture, and which served as a design template for theengineering of ZFNs targeted to maize IPP2K.

FIG. 65, panels A to E, depict a ZFN Expression vector cloning scheme. Astepwise cloning strategy was used to generate ZFN expressionconstructs. Individual ZFN-encoding genes were cloned into vectorspVAX-N2A-NLSop2-EGFP-FokMono (A) and pVAX-C2A-NLSop2-EGFP-FokMono (B) tocreate a dual-protein cassette (C). This cassette was ligated intopDAB3872 (D) to generate a final plasmid (E) for expression of the ZFNheterodimer.

FIG. 66 depicts ZFN binding in a maize IPP2K gene. Two ZFN proteins arerequired to carry out double-stranded cleavage of DNA. The sequencesurrounding the cleavage site (indicated with a downward arrow) is shown(SEQ ID NO:7). One protein (8075) was bound to sequence CTGTGGGGCCAT(top strand) (SEQ ID NO:8), where another protein (8684, 8685, or 8686)bound to downstream sequence (CTTGACCAACTCAGCCAG, bottom strand) (SEQ IDNO:9).

FIG. 67 depicts sequences of wild-type (top sequence, SEQ ID NO:10) andZFN clone 127 (bottom sequence, SEQ ID NO:11). The cleavage target forthis ZFN is highlighted in a gray box.

FIG. 68 shows an alignment of multiple deletions resulting fromnon-homologous end joining (NHEJ) of a ZFN-mediated dsDNA break in themaize IPP2K gene as detecting by 454 sequencing. The cleavage target forthis ZFN is highlighted in a gray box.

FIG. 69 is a graph depicting gene correction rates in the GFP cellreporter assay system described in U.S. Patent No. 2005/0064474 andherein. The ZFN pairs tested in each sample are shown below each bar.

FIG. 70 depicts plasmid pDAB7471, constructed as described in Example18B.

FIG. 71 depicts plasmid pDAB7451, constructed as described in Example18C.

FIG. 72 is a schematic depicting an exemplary autonomousherbicide-tolerance gene expression cassette. This constructioncomprises a complete promoter-transcriptional unit (PTU) containing apromoter, herbicide tolerance gene and poly adenylation (polyA)termination sequence as described in Example 18D.

FIG. 73 depicts plasmid pDAB7422, constructed as described in Example18E. The plasmid includes a complete promoter-transcriptional unit (PTU)containing a promoter, herbicide tolerance gene and poly adenylation(polyA) termination sequence inserted into a position-1 plasmidbackbone.

FIG. 74 depicts plasmid pDAB7452, constructed as described in Example18E. The plasmid includes a complete promoter-transcriptional unit (PTU)containing a promoter, herbicide tolerance gene and poly adenylation(polyA) termination sequence inserted into a position-2 plasmidbackbone.

FIG. 75 is a schematic depicting an exemplary non-autonomousherbicide-tolerance gene expression cassette. This constructioncomprises an incomplete promoter-transcriptional unit (PTU) containing aherbicide tolerance gene and poly adenylation (polyA) terminationsequence as described in Example 18F.

FIG. 76 depicts plasmid pDAB7423, constructed as described in Example18G. This plasmid includes an incomplete promoter-transcriptional unit(PTU) containing an herbicide tolerance gene and poly adenylation(polyA) termination sequence inserted into a position-1 plasmidbackbone.

FIG. 77 depicts plasmid pDAB7454, constructed as described in Example18G. The plasmid includes an incomplete promoter-transcriptional unit(PTU) containing an herbicide tolerance gene and poly adenylation(polyA) termination sequence inserted into a position-2 plasmid backboneas described in Example 18G.

FIG. 78 depicts plasmid pDAB 7424 (an exemplary Gateway®-adaptedposition-1 autonomous donor), constructed as described in Example 18H.

FIG. 79 depicts plasmid pDAB 7425 (an exemplary Gateway®-adaptedposition-1 autonomous donor), constructed as described in Example 18H.

FIG. 80 depicts plasmid pDAB 7426, constructed as described in Example18H. pDAB 7426 is a combination plasmid containing the position-1autonomous donor with a ZFN-expression cassette.

FIG. 81 depicts plasmid pDAB 7427, constructed as described in Example18H. pDAB 7427 is a combination plasmid containing the position-1autonomous donor with a ZFN-expression cassette.

FIG. 82 depicts amplification of donor-DNA specific sequences fromgenomic DNA. The presence of a 317 bp product is diagnostic for thepresence of donor DNA containing the PAT gene inserted into the genomeof maize calli lines #61-72 as described in Example 20C. HiII indicatesa wild-type negative control.

FIG. 83 depicts amplification of the 5′-boundary between donor-DNA andmaize genomic sequences specific for IPP2K. Secondary PCR productsderived from targeted integration of donor into the IPP2K gene werediagnosed by the presence of DNA fragments of 1.65 Kbp as described inExample 21A. HiII indicates a wild-type negative control.

FIG. 84 depicts amplification of the 3′-boundary between donor-DNA andmaize genomic sequences specific for IPP2K. Secondary PCR productsderived from targeted integration of donor into the IPP2K gene werediagnosed by the presence of DNA fragments of 1.99 Kbp as described inExample 21A. HiII indicates a wild-type negative control.

FIG. 85 depicts amplification of the upstream (5′-) boundary betweengenome and donor. PCR products derived from targeted integration ofdonor into the IPP2K gene (5′-boundary) were diagnosed by the presenceof DNA fragments 1.35 Kbp in size as described in Example 21B. HiIIindicates a wild-type negative control.

FIG. 86 depicts amplification of the downstream (3′-) boundary betweendonor and genome. PCR products derived from targeted integration ofdonor into the IPP2K gene (3′-boundary) were diagnosed by the presenceof DNA fragments 1.66 Kbp in size as described in Example 21B. HiIIindicates a wild-type negative control.

FIG. 87 depicts the sequence of the position-1 5′-homology flank (SEQ IDNO:171).

FIG. 88 depicts the sequence of the position-1 3′-homology flank (SEQ IDNO:172).

FIG. 89 depicts the sequence of the position-2 5′-homology flank (SEQ IDNO:139).

FIG. 90 depicts the sequence of the position-2 3′-homology flank (SEQ IDNO:140).

FIG. 91 depicts the sequence of an upstream (5′-) IPP2K genomic sequenceof the ZFN targeted regions (SEQ ID NO:141).

FIG. 92 depicts the sequence of a downstream (3′-) IPP2K genomicsequence of the ZFN targeted regions (SEQ ID NO: 142).

DETAILED DESCRIPTION

Disclosed herein are compositions comprising zinc finger bindingpolypeptides (ZFPs) containing non-canonical zinc fingers of the formatCys-Cys-His-Cys. Inasmuch as zinc coordination provides the principalfolding energy for zinc fingers, adjustment of zinc coordinatingresidues provides a ready means for modifying finger stability andstructure, which impacts on a variety of important functional featuresof zinc finger proteins, including, for example, cellular half life,interactions with other cellular factors, DNA binding specificity andaffinity, and relative orientation of functional domains.

Zinc finger proteins comprising non-canonical zinc fingers such as thosedisclosed in U.S. Patent Application Nos. 20030108880; 20060246567; and20060246588 have been shown to bind DNA and alter transcription.However, when incorporated into zinc finger nucleases (ZFNs, see, forexample US Patent Application Publication No. 2005/0064474), thesepreviously described non-canonical zinc finger proteins can sometimesexhibit sub-optimal activity in cleaving the target DNA.

Described herein are zinc finger proteins comprising one or more CCHCzinc fingers, in which specific sequences surrounding the C-terminalpair of zinc coordinating residues have been altered. Also describedherein are fusion proteins, for example zinc finger nucleases (ZFNs),comprising these optimized non-canonical zinc fingers, wherein the ZFNscleave the target DNA at rates comparable to cleavage achieved usingZFNs comprising canonical (CCHH) zinc fingers.

Fusion polypeptides, as disclosed herein, can enhance or suppresstranscription of a gene, and/or cleave a target sequence.Polynucleotides encoding optimized non-canonical zinc fingers, andpolynucleotides encoding fusion proteins comprising one or moreoptimized non-canonical zinc fingers are also provided. Additionallyprovided are pharmaceutical compositions comprising a therapeuticallyeffective amount of any of the zinc finger-nucleotide bindingpolypeptides described herein or functional fragments thereof; or atherapeutically effective amount of a nucleotide sequence that encodesany of the modified zinc finger-nucleotide binding polypeptides orfunctional fragments thereof, in combination with a pharmaceuticallyacceptable carrier. Further provided are agricultural compositionscomprising an agronomically effective amount of any of the zincfinger-nucleotide binding polypeptides described herein or functionalfragments thereof; or an agronomically effective amount of a nucleotidesequence that encodes any of the modified zinc finger-nucleotide bindingpolypeptides or functional fragments thereof, in combination with anagriculturally acceptable carrier. Also provided are screening methodsfor obtaining a modified zinc finger-nucleotide binding polypeptidewhich binds to a genomic sequence.

Genomic sequences include those present in chromosomes, episomes,organellar genomes (e.g., mitochondria, chloroplasts), artificialchromosomes and any other type of nucleic acid present in a cell suchas, for example, amplified sequences, double minute chromosomes and thegenomes of endogenous or infecting bacteria and viruses. Genomicsequences can be normal (i.e., wild-type) or mutant; mutant sequencescan comprise, for example, insertions, deletions, substitutions,translocations, rearrangements, and/or point mutations. A genomicsequence can also comprise one of a number of different alleles.

General

Practice of the methods, as well as preparation and use of thecompositions disclosed herein employ, unless otherwise indicated,conventional techniques in molecular biology, biochemistry, chromatinstructure and analysis, computational chemistry, cell culture,recombinant DNA and related fields as are within the skill of the art.These techniques are fully explained in the literature. See, forexample, Sambrook et al. MOLECULAR CLONING: A LABORATORY MANUAL, Secondedition, Cold Spring Harbor Laboratory Press, 1989 and Third edition,2001; Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley& Sons, New York, 1987 and periodic updates; the series METHODS INENZYMOLOGY, Academic Press, San Diego; Wolffe, CHROMATIN STRUCTURE ANDFUNCTION, Third edition, Academic Press, San Diego, 1998; METHODS INENZYMOLOGY, Vol. 304, “Chromatin” (P. M. Wassarman and A. P. Wolffe,eds.), Academic Press, San Diego, 1999; and METHODS IN MOLECULARBIOLOGY, Vol. 119, “Chromatin Protocols” (P. B. Becker, ed.) HumanaPress, Totowa, 1999.

Definitions

The terms “nucleic acid,” “polynucleotide,” and “oligonucleotide” areused interchangeably and refer to a deoxyribonucleotide orribonucleotide polymer, in linear or circular conformation, and ineither single- or double-stranded form. For the purposes of the presentdisclosure, these terms are not to be construed as limiting with respectto the length of a polymer. The terms can encompass known analogues ofnatural nucleotides, as well as nucleotides that are modified in thebase, sugar and/or phosphate moieties (e.g., phosphorothioatebackbones). In general, an analogue of a particular nucleotide has thesame base-pairing specificity; i.e., an analogue of A will base-pairwith T.

The terms “polypeptide,” “peptide” and “protein” are usedinterchangeably to refer to a polymer of amino acid residues. The termalso applies to amino acid polymers in which one or more amino acids arechemical analogues or modified derivatives of a correspondingnaturally-occurring amino acids.

“Binding” refers to a sequence-specific, non-covalent interactionbetween macromolecules (e.g., between a protein and a nucleic acid). Notall components of a binding interaction need be sequence-specific (e.g.,contacts with phosphate residues in a DNA backbone), as long as theinteraction as a whole is sequence-specific. Such interactions aregenerally characterized by a dissociation constant (K_(d)) of 10⁻⁶ M⁻¹or lower. “Affinity” refers to the strength of binding: increasedbinding affinity being correlated with a lower K_(d.)

A “binding protein” is a protein that is able to bind non-covalently toanother molecule. A binding protein can bind to, for example, a DNAmolecule (a DNA-binding protein), an RNA molecule (an RNA-bindingprotein) and/or a protein molecule (a protein-binding protein). In thecase of a protein-binding protein, it can bind to itself (to formhomodimers, homotrimers, etc.) and/or it can bind to one or moremolecules of a different protein or proteins. A binding protein can havemore than one type of binding activity. For example, zinc fingerproteins have DNA-binding, RNA-binding and protein-binding activity.

A “zinc finger DNA binding protein” (or binding domain) is a protein, ora domain within a larger protein, that binds DNA in a sequence-specificmanner through one or more zinc fingers, which are regions of amino acidsequence within the binding domain whose structure is stabilized throughcoordination of a zinc ion. The term zinc finger DNA binding protein isoften abbreviated as zinc finger protein or ZFP.

Zinc finger binding domains can be “engineered” to bind to apredetermined nucleotide sequence. Non-limiting examples of methods forengineering zinc finger proteins are design and selection. A designedzinc finger protein is a protein not occurring in nature whosedesign/composition results principally from rational criteria. Rationalcriteria for design include application of substitution rules andcomputerized algorithms for processing information in a database storinginformation of existing ZFP designs and binding data. See, for example,U.S. Pat. Nos. 6,140,081; 6,453,242; 6,534,261; and 6,785,613; see, alsoWO 98/53058; WO 98/53059; WO 98/53060; WO 02/016536 and WO 03/016496;and U.S. Pat. Nos. 6,746,838; 6,866,997; and 7,030,215.

A “selected” zinc finger protein is a protein not found in nature whoseproduction results primarily from an empirical process such as phagedisplay, interaction trap or hybrid selection. See e.g., U.S. Pat. No.5,789,538; U.S. Pat. No. 5,925,523; U.S. Pat. No. 6,007,988; U.S. Pat.No. 6,013,453; U.S. Pat. No. 6,200,759; U.S. Pat. No. 6,733,970; U.S.Pat. No. RE39,229; and WO 95/19431; WO 96/06166; WO 98/53057; WO98/54311; WO 00/27878; WO 01/60970 WO 01/88197 and WO 02/099084.

A “non-canonical” zinc finger protein is a protein comprising anon-canonical (non-C2H2) zinc finger. A non-canonical zinc finger thuscomprises a substitution, addition and/or deletion of at least one aminoacid, compared to a naturally occurring C2H2 zinc finger protein.Non-limiting examples of non-canonical zinc fingers include thosecomprising zinc coordinating residues (from amino to carboxy) ofCys-Cys-His-Cys (e.g., C3H).

A “homologous sequence” refers to a first sequence which shares a degreeof sequence identity with a second sequence, and whose sequence may beidentical to that of the second sequence. A “homologous, non-identicalsequence” refers to a first sequence which shares a degree of sequenceidentity with a second sequence, but whose sequence is not identical tothat of the second sequence. For example, a polynucleotide comprisingthe wild-type sequence of a mutant gene is homologous and non-identicalto the sequence of the mutant gene. In certain embodiments, the degreeof homology between the two sequences is sufficient to allow homologousrecombination therebetween, utilizing normal cellular mechanisms. Twohomologous non-identical sequences can be any length and their degree ofnon-homology can be as small as a single nucleotide (e.g., forcorrection of a genomic point mutation by targeted homologousrecombination) or as large as 10 or more kilobases (e.g., for insertionof a gene at a predetermined site in a chromosome). Two polynucleotidescomprising the homologous non-identical sequences need not be the samelength. For example, an exogenous polynucleotide (i.e., donorpolynucleotide) of between 20 and 10,000 nucleotides or nucleotide pairscan be used.

Techniques for determining nucleic acid and amino acid sequence identityare known in the art. Typically, such techniques include determining thenucleotide sequence of the mRNA for a gene and/or determining the aminoacid sequence encoded thereby, and comparing these sequences to a secondnucleotide or amino acid sequence. Genomic sequences can also bedetermined and compared in this fashion. In general, identity refers toan exact nucleotide-to-nucleotide or amino acid-to-amino acidcorrespondence of two polynucleotides or polypeptide sequences,respectively. Two or more sequences (polynucleotide or amino acid) canbe compared by determining their percent identity. The percent identityof two sequences, whether nucleic acid or amino acid sequences, is thenumber of exact matches between two aligned sequences divided by thelength of the shorter sequences and multiplied by 100. An approximatealignment for nucleic acid sequences is provided by the local homologyalgorithm of Smith and Waterman, Advances in Applied Mathematics2:482-489 (1981). This algorithm can be applied to amino acid sequencesby using the scoring matrix developed by Dayhoff, Atlas of ProteinSequences and Structure, M. O. Dayhoff ed., 5 suppl. 3:353-358, NationalBiomedical Research Foundation, Washington, D.C., USA, and normalized byGribskov, Nucl. Acids Res. 14(6):6745-6763 (1986). An exemplaryimplementation of this algorithm to determine percent identity of asequence is provided by the Genetics Computer Group (Madison, Wis.) inthe “BestFit” utility application. The default parameters for thismethod are described in the Wisconsin Sequence Analysis Package ProgramManual, Version 8 (1995) (available from Genetics Computer Group,Madison, Wis.). An exemplary method of establishing percent identity inthe context of the present disclosure is to use the MPSRCH package ofprograms copyrighted by the University of Edinburgh, developed by JohnF. Collins and Shane S. Sturrok, and distributed by IntelliGenetics,Inc. (Mountain View, Calif.). From this suite of packages theSmith-Waterman algorithm can be employed where default parameters areused for the scoring table (for example, gap open penalty of 12, gapextension penalty of one, and a gap of six). From the data generated the“Match” value reflects sequence identity. Other suitable programs forcalculating the percent identity or similarity between sequences aregenerally known in the art, for example, another alignment program isBLAST, used with default parameters. For example, BLASTN and BLASTP canbe used using the following default parameters: genetic code=standard;filter=none; strand=both; cutoff=60; expect=10; Matrix=BLOSUM62;Descriptions=50 sequences; sort by=HIGH SCORE; Databases=non-redundant,GenBank+EMBL+DDBJ+PDB+GenBank CDS translations+Swissprotein+Spupdate+PIR. Details of these programs can be found on theinternet. With respect to sequences described herein, the range ofdesired degrees of sequence identity is approximately 35% to 100% andany integer value therebetween. Typically the percent identities betweensequences are at least 35%-40%; 40%-45%; 45%-50%; 50%-60%; 60%-70%;70-75%, preferably 80-82%, more preferably 85-90%, even more preferably92%, still more preferably 95%, and most preferably 98% sequenceidentity.

Alternatively, the degree of sequence similarity between polynucleotidescan be determined by hybridization of polynucleotides under conditionsthat allow formation of stable duplexes between homologous regions,followed by digestion with single-stranded-specific nuclease(s), andsize determination of the digested fragments. Two nucleic acid, or twopolypeptide sequences are substantially homologous to each other whenthe sequences exhibit at least about 70%-75%, preferably 80%-82%, morepreferably 85%-90%, even more preferably 92%, still more preferably 95%,and most preferably 98% sequence identity over a defined length of themolecules, as determined using the methods above. As used herein,substantially homologous also refers to sequences showing completeidentity to a specified DNA or polypeptide sequence. DNA sequences thatare substantially homologous can be identified in a Southernhybridization experiment under, for example, stringent conditions, asdefined for that particular system. Defining appropriate hybridizationconditions is within the skill of the art. See, e.g., Sambrook et al.,supra; Nucleic Acid Hybridization: A Practical Approach, editors B. D.Hames and S. J. Higgins, (1985) Oxford; Washington, D.C.; IRL Press).

Selective hybridization of two nucleic acid fragments can be determinedas follows. The degree of sequence identity between two nucleic acidmolecules affects the efficiency and strength of hybridization eventsbetween such molecules. A partially identical nucleic acid sequence willat least partially inhibit the hybridization of a completely identicalsequence to a target molecule. Inhibition of hybridization of thecompletely identical sequence can be assessed using hybridization assaysthat are well known in the art (e.g., Southern (DNA) blot, Northern(RNA) blot, solution hybridization, or the like, see Sambrook, et al.,Molecular Cloning: A Laboratory Manual, Second Edition, (1989) ColdSpring Harbor, N.Y.). Such assays can be conducted using varying degreesof selectivity, for example, using conditions varying from low to highstringency. If conditions of low stringency are employed, the absence ofnon-specific binding can be assessed using a secondary probe that lackseven a partial degree of sequence identity (for example, a probe havingless than about 30% sequence identity with the target molecule), suchthat, in the absence of non-specific binding events, the secondary probewill not hybridize to the target.

When utilizing a hybridization-based detection system, a nucleic acidprobe is chosen that is complementary to a reference nucleic acidsequence, and then by selection of appropriate conditions the probe andthe reference sequence selectively hybridize, or bind, to each other toform a duplex molecule. A nucleic acid molecule that is capable ofhybridizing selectively to a reference sequence under moderatelystringent hybridization conditions typically hybridizes under conditionsthat allow detection of a target nucleic acid sequence of at least about10-14 nucleotides in length having at least approximately 70% sequenceidentity with the sequence of the selected nucleic acid probe. Stringenthybridization conditions typically allow detection of target nucleicacid sequences of at least about 10-14 nucleotides in length having asequence identity of greater than about 90-95% with the sequence of theselected nucleic acid probe. Hybridization conditions useful forprobe/reference sequence hybridization, where the probe and referencesequence have a specific degree of sequence identity, can be determinedas is known in the art (see, for example, Nucleic Acid Hybridization: APractical Approach, editors B. D. Hames and S. J. Higgins, (1985)Oxford; Washington, D.C.; IRL Press).

Conditions for hybridization are well-known to those of skill in theart. Hybridization stringency refers to the degree to whichhybridization conditions disfavor the formation of hybrids containingmismatched nucleotides, with higher stringency correlated with a lowertolerance for mismatched hybrids. Factors that affect the stringency ofhybridization are well-known to those of skill in the art and include,but are not limited to, temperature, pH, ionic strength, andconcentration of organic solvents such as, for example, formamide anddimethylsulfoxide. As is known to those of skill in the art,hybridization stringency is increased by higher temperatures, lowerionic strength and lower solvent concentrations.

With respect to stringency conditions for hybridization, it is wellknown in the art that numerous equivalent conditions can be employed toestablish a particular stringency by varying, for example, the followingfactors: the length and nature of the sequences, base composition of thevarious sequences, concentrations of salts and other hybridizationsolution components, the presence or absence of blocking agents in thehybridization solutions (e.g., dextran sulfate, and polyethyleneglycol), hybridization reaction temperature and time parameters, as wellas, varying wash conditions. The selection of a particular set ofhybridization conditions is selected following standard methods in theart (see, for example, Sambrook, et al., Molecular Cloning: A LaboratoryManual, Second Edition, (1989) Cold Spring Harbor, N.Y.).

“Recombination” refers to a process of exchange of genetic informationbetween two polynucleotides. For the purposes of this disclosure,“homologous recombination (HR)” refers to the specialized form of suchexchange that takes place, for example, during repair of double-strandbreaks in cells. This process requires nucleotide sequence homology,uses a “donor” molecule to template repair of a “target” molecule (i.e.,the one that experienced the double-strand break), and is variouslyknown as “non-crossover gene conversion” or “short tract geneconversion,” because it leads to the transfer of genetic informationfrom the donor to the target. Without wishing to be bound by anyparticular theory, such transfer can involve mismatch correction ofheteroduplex DNA that forms between the broken target and the donor,and/or “synthesis-dependent strand annealing,” in which the donor isused to resynthesize genetic information that will become part of thetarget, and/or related processes. Such specialized HR often results inan alteration of the sequence of the target molecule such that part orall of the sequence of the donor polynucleotide is incorporated into thetarget polynucleotide.

“Cleavage” refers to the breakage of the covalent backbone of a DNAmolecule. Cleavage can be initiated by a variety of methods including,but not limited to, enzymatic or chemical hydrolysis of a phosphodiesterbond. Both single-stranded cleavage and double-stranded cleavage arepossible, and double-stranded cleavage can occur as a result of twodistinct single-stranded cleavage events. DNA cleavage can result in theproduction of either blunt ends or staggered ends. In certainembodiments, fusion polypeptides are used for targeted double-strandedDNA cleavage.

A “cleavage domain” comprises one or more polypeptide sequences whichpossesses catalytic activity for DNA cleavage. A cleavage domain can becontained in a single polypeptide chain or cleavage activity can resultfrom the association of two (or more) polypeptides.

A “cleavage half-domain” is a polypeptide sequence which, in conjunctionwith a second polypeptide (either identical or different) forms acomplex having cleavage activity (e.g., double-strand cleavageactivity).

The terms “cleavage domain” and “cleavage half-domain” includeswild-type domains and portions or mutants of cleavage domains orcleavage half-domains that retains the ability to multimerize (e.g.,dimerize) to form a functional cleavage domain.

“Chromatin” is the nucleoprotein structure comprising the cellulargenome. Cellular chromatin comprises nucleic acid, primarily DNA, andprotein, including histones and non-histone chromosomal proteins. Themajority of eukaryotic cellular chromatin exists in the form ofnucleosomes, wherein a nucleosome core comprises approximately 150 basepairs of DNA associated with an octamer comprising two each of histonesH2A, H2B, H3 and H4; and linker DNA (of variable length depending on theorganism) extends between nucleosome cores. A molecule of histone H1 isgenerally associated with the linker DNA. For the purposes of thepresent disclosure, the term “chromatin” is meant to encompass all typesof cellular nucleoprotein, both prokaryotic and eukaryotic. Cellularchromatin includes both chromosomal and episomal chromatin.

A “chromosome,” is a chromatin complex comprising all or a portion ofthe genome of a cell. The genome of a cell is often characterized by itskaryotype, which is the collection of all the chromosomes that comprisethe genome of the cell. The genome of a cell can comprise one or morechromosomes.

An “episome” is a replicating nucleic acid, nucleoprotein complex orother structure comprising a nucleic acid that is not part of thechromosomal karyotype of a cell. Examples of episomes include plasmidsand certain viral genomes.

An “accessible region” is a site in cellular chromatin in which a targetsite present in the nucleic acid can be bound by an exogenous moleculewhich recognizes the target site. Without wishing to be bound by anyparticular theory, it is believed that an accessible region is one thatis not packaged into a nucleosomal structure. The distinct structure ofan accessible region can often be detected by its sensitivity tochemical and enzymatic probes, for example, nucleases.

A “target site” or “target sequence” is a nucleic acid sequence thatdefines a portion of a nucleic acid to which a binding molecule willbind, provided sufficient conditions for binding exist. For example, thesequence 5′-GAATTC-3′ is a target site for the Eco RI restrictionendonuclease.

An “exogenous” molecule is a molecule that is not normally present in acell, but can be introduced into a cell by one or more genetic,biochemical or other methods. “Normal presence in the cell” isdetermined with respect to the particular developmental stage andenvironmental conditions of the cell. Thus, for example, a molecule thatis present only during embryonic development of muscle is an exogenousmolecule with respect to an adult muscle cell. Similarly, a moleculeinduced by heat shock is an exogenous molecule with respect to anon-heat-shocked cell. An exogenous molecule can comprise, for example,a functioning version of a malfunctioning endogenous molecule or amalfunctioning version of a normally-functioning endogenous molecule.

An exogenous molecule can be, among other things, a small molecule, suchas is generated by a combinatorial chemistry process, or a macromoleculesuch as a protein, nucleic acid, carbohydrate, lipid, glycoprotein,lipoprotein, polysaccharide, any modified derivative of the abovemolecules, or any complex comprising one or more of the above molecules.Nucleic acids include DNA and RNA, can be single- or double-stranded;can be linear, branched or circular; and can be of any length. Nucleicacids include those capable of forming duplexes, as well astriplex-forming nucleic acids. See, for example, U.S. Pat. Nos.5,176,996 and 5,422,251. Proteins include, but are not limited to,DNA-binding proteins, transcription factors, chromatin remodelingfactors, methylated DNA binding proteins, polymerases, methylases,demethylases, acetylases, deacetylases, kinases, phosphatases,integrases, recombinases, ligases, topoisomerases, gyrases andhelicases.

An exogenous molecule can be the same type of molecule as an endogenousmolecule, e.g., an exogenous protein or nucleic acid. For example, anexogenous nucleic acid can comprise an infecting viral genome, anAgrogacterium tumefacians T-strand, a plasmid or episome introduced intoa cell, or a chromosome that is not normally present in the cell.Exogenous nucleic acids or polynucleotides can, however, containsequences that are homologous or identical to endogenous sequences. Withrespect to a particular endogenous genomic region, an “exogenoussequence” refers to a nucleotide sequence that is not present at thatregion. Such an exogenous sequence may be present at another endogenouschromosomal location or it may not be present in the genome at all.Thus, an exogenous polynucleotide can contain both exogenous andendogenous sequences: for example, a transgene flanked by sequenceshomologous to a genomic region. Such exogenous nucleic acids are used inmethods for targeted integration and targeted recombination as describedinfra. Methods for the introduction of exogenous molecules into cellsare known to those of skill in the art and include, but are not limitedto, lipid-mediated transfer (i.e., liposomes, including neutral andcationic lipids), electroporation, direct injection, cell fusion,particle bombardment, calcium phosphate co-precipitation,DEAE-dextran-mediated transfer and viral vector-mediated transfer.

By contrast, an “endogenous” molecule is one that is normally present ina particular cell at a particular developmental stage under particularenvironmental conditions. For example, an endogenous nucleic acid cancomprise a chromosome, the genome of a mitochondrion, chloroplast orother organelle, or a naturally-occurring episomal nucleic acid.Additional endogenous molecules can include proteins, for example,transcription factors and enzymes.

A “fusion” molecule is a molecule in which two or more subunit moleculesare linked, for example, covalently. The subunit molecules can be thesame chemical type of molecule, or can be different chemical types ofmolecules. Examples of the first type of fusion molecule include, butare not limited to, fusion proteins (for example, a fusion between a ZFPDNA-binding domain and a cleavage domain) and fusion nucleic acids (forexample, a nucleic acid encoding the fusion protein described supra).Examples of the second type of fusion molecule include, but are notlimited to, a fusion between a triplex-forming nucleic acid and apolypeptide, and a fusion between a minor groove binder and a nucleicacid.

Expression of a fusion protein in a cell can result from delivery of thefusion protein to the cell or by delivery of a polynucleotide encodingthe fusion protein to a cell, wherein the polynucleotide is transcribed,and the transcript is translated, to generate the fusion protein.Trans-splicing, polypeptide cleavage and polypeptide ligation can alsobe involved in expression of a protein in a cell. Methods forpolynucleotide and polypeptide delivery to cells are presented elsewherein this disclosure.

A “gene,” for the purposes of the present disclosure, includes a DNAregion encoding a gene product (see infra), as well as all DNA regionswhich regulate the production of the gene product, whether or not suchregulatory sequences are adjacent to coding and/or transcribedsequences. Accordingly, a gene includes, but is not necessarily limitedto, promoter sequences, terminators, translational regulatory sequencessuch as ribosome binding sites and internal ribosome entry sites,enhancers, silencers, insulators, boundary elements, replicationorigins, matrix attachment sites and locus control regions.

“Gene expression” refers to the conversion of the information, containedin a gene, into a gene product. A gene product can be the directtranscriptional product of a gene (e.g., mRNA, tRNA, rRNA, antisenseRNA, ribozyme, structural RNA or any other type of RNA) or a proteinproduced by translation of a mRNA. Gene products also include RNAs whichare modified, by processes such as capping, polyadenylation,methylation, and editing, and proteins modified by, for example,methylation, acetylation, phosphorylation, ubiquitination,ADP-ribosylation, myristilation, and glycosylation.

“Modulation” of gene expression refers to a change in the activity of agene. Modulation of expression can include, but is not limited to, geneactivation and gene repression.

“Plant” cells include, but are not limited to, cells of monocotyledonous(monocots) or dicotyledonous (dicots) plants. Non-limiting examples ofmonocots include cereal plants such as maize, rice, barley, oats, wheat,sorghum, rye, sugarcane, pineapple, onion, banana, and coconut.Non-limiting examples of dicots include tobacco, tomato, sunflower,cotton, sugarbeet, potato, lettuce, melon, soybean, canola (rapeseed),and alfalfa. Plant cells may be from any part of the plant and/or fromany stage of plant development.

A “region of interest” is any region of cellular chromatin, such as, forexample, a gene or a non-coding sequence within or adjacent to a gene,in which it is desirable to bind an exogenous molecule. Binding can befor the purposes of targeted DNA cleavage and/or targeted recombination.A region of interest can be present in a chromosome, an episome, anorganellar genome (e.g., mitochondrial, chloroplast), or an infectingviral genome, for example. A region of interest can be within the codingregion of a gene, within transcribed non-coding regions such as, forexample, leader sequences, trailer sequences or introns, or withinnon-transcribed regions, either upstream or downstream of the codingregion. A region of interest can be as small as a single nucleotide pairor up to 25,000 nucleotide pairs in length, or any integral value ofnucleotide pairs.

The terms “operative linkage” and “operatively linked” (or “operablylinked”) are used interchangeably with reference to a juxtaposition oftwo or more components (such as sequence elements), in which thecomponents are arranged such that both components function normally andallow the possibility that at least one of the components can mediate afunction that is exerted upon at least one of the other components. Byway of illustration, a transcriptional regulatory sequence, such as apromoter, is operatively linked to a coding sequence if thetranscriptional regulatory sequence controls the level of transcriptionof the coding sequence in response to the presence or absence of one ormore transcriptional regulatory factors. A transcriptional regulatorysequence is generally operatively linked in cis with a coding sequence,but need not be directly adjacent to it. For example, an enhancer is atranscriptional regulatory sequence that is operatively linked to acoding sequence, even though they are not contiguous.

With respect to fusion polypeptides, the term “operatively linked” canrefer to the fact that each of the components performs the same functionin linkage to the other component as it would if it were not so linked.For example, with respect to a fusion polypeptide in which a ZFPDNA-binding domain is fused to a cleavage domain, the ZFP DNA-bindingdomain and the cleavage domain are in operative linkage if, in thefusion polypeptide, the ZFP DNA-binding domain portion is able to bindits target site and/or its binding site, while the cleavage domain isable to cleave DNA in the vicinity of the target site.

A “functional fragment” of a protein, polypeptide or nucleic acid is aprotein, polypeptide or nucleic acid whose sequence is not identical tothe full-length protein, polypeptide or nucleic acid, yet retains thesame function as the full-length protein, polypeptide or nucleic acid. Afunctional fragment can possess more, fewer, or the same number ofresidues as the corresponding native molecule, and/or can contain oneore more amino acid or nucleotide substitutions. Methods for determiningthe function of a nucleic acid (e.g., coding function, ability tohybridize to another nucleic acid) are well-known in the art. Similarly,methods for determining protein function are well-known. For example,the DNA-binding function of a polypeptide can be determined, forexample, by filter-binding, electrophoretic mobility-shift, orimmunoprecipitation assays. DNA cleavage can be assayed by gelelectrophoresis. See Ausubel et al., supra. The ability of a protein tointeract with another protein can be determined, for example, byco-immunoprecipitation, two-hybrid assays or complementation, bothgenetic and biochemical. See, for example, Fields et al. (1989) Nature340:245-246; U.S. Pat. No. 5,585,245 and PCT WO 98/44350.

Zinc Finger Binding Domains

Described herein are non-canonical zinc finger binding domains andpolynucleotides encoding these zinc finger binding domains. In certainembodiments, the non-canonical zinc finger binding domains describedherein are C3H zinc fingers, in which one of the two conservedzinc-coordinating histidine residues is converted to cysteine. Inadditional embodiments, the C-terminal-most histidine residue isconverted to a cysteine residue, generating a “CCHC protein.”

A zinc finger binding domain can comprise one or more zinc fingers(e.g., 2, 3, 4, 5, 6, 7, 8, 9 or more zinc fingers), and can beengineered to bind to any target sequence (e.g., a genomic sequence).Zinc finger binding domains may bind to DNA, RNA and/or protein.Typically, a single zinc finger domain is about 30 amino acids inlength. Zinc fingers include both canonical C₂H₂ zinc fingers (i.e.,those in which the zinc ion is coordinated by two cysteine and twohistidine residues) and non-canonical zinc fingers including, forexample, C₃H zinc fingers (those in which the zinc ion is coordinated bythree cysteine residues and one histidine residue). See also U.S. PatentApplication Nos. 20030108880, 20060246567 and 20060246588; thedisclosures of which are incorporated by reference.

Structural studies have demonstrated that a canonical zinc finger domain(motif) contains two beta sheets (held in a beta turn which contains thetwo invariant cysteine residues) and an alpha helix (containing the twoinvariant histidine residues), which are held in a particularconformation through coordination of a zinc atom by the two cysteinesand the two histidines. The non-canonical zinc fingers disclosed hereinretain this beta-beta-alpha structure.

The non-canonical zinc fingers described herein may be naturallyoccurring zinc finger binding domains. However, more typically,non-canonical zinc fingers as described herein include one or more zincfinger components in which at least one of the zinc-coordinatingcysteine or histidine residues has been replaced with one or more aminoacids. For example, in certain embodiments, the C-terminal His residueof a canonical zinc finger binding module is replaced with a Cysresidue.

The CCHC zinc fingers described herein can also comprise one or morealterations (with respect to the sequence of a naturally-occurring C2H2zinc finger) in the sequence of amino acids residues other than the zinccoordinating residues. Such alterations can comprise substitutions,deletions, and/or insertions. Amino acids may be altered anywhere in thezinc finger. Non-limiting examples of alterations include: (1)substitutions of single residues surrounding the alteredzinc-coordinating residue; (2) addition of extra residues before orafter the altered zinc-coordinating residue, (e.g., in cases in whichthe C-terminal-most His residue is converted to Cys, addition of extraamino acid residues may facilitate zinc coordination by compensating forthe shorter cysteine side chain); and/or (3) substitution of residueslocated between the His and Cys residues of a naturally-occurring CCHCzinc finger into the corresponding region of a non-canonical CCHC zincfinger.

In certain embodiments, the zinc finger proteins described hereininclude at least one zinc finger comprising a non-canonical (non-C₂H₂)zinc finger, wherein the non-canonical zinc finger has a helical portioninvolved in DNA binding and wherein the zinc-coordinating region of thehelical portion comprises the amino acid sequence HX₁X₂RCX_(L) (SEQ IDNO:2); and wherein the zinc finger protein is engineered to bind to atarget sequence. In certain embodiments, X₁ is A or K or T; X₂ is Q or Eor R; and X_(L) is G.

In other embodiments, the non-canonical zinc fingers described hereinhave the general structure:Cys-(X^(A))₂₋₄-Cys-(X^(B))₁₂-His-(X^(C))₃₋₅-Cys-(X^(D))₁₋₁₀ (SEQ IDNO:3), where X^(A), X^(B), X^(C) and X^(D) represent any amino acid. Inembodiments in which X^(C) comprises 3 residues (i) at least one ofthese residues is altered as compared to a canonical CCHC zinc finger;and/or (ii) X^(D) comprises at least one deletion, substitution orinsertion as compared to a canonical CCHH zinc finger. In certainembodiments, X^(D) comprises the sequence QLV or QKP. In otherembodiments X^(D) comprises one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8,9, or 10) Gly (G) residues.

Partial amino acid sequence (including and C-terminal to the 3^(rd) zinccoordinating residue) of exemplary non-canonical zinc fingers are shownin Tables 1, 2, 3 and 4. In all Tables, the two C-terminal-most (i.e.,the third and fourth) zinc coordinating residues (H and C) areunderlined. The alterations (e.g., substitutions, insertions, deletions)as compared to the sequence of the “wild-type” non-canonical finger (Row2 of Tables 1 and 3) are shown in double underlining.

TABLE 1 C2H2 HTKIHLRGSQLV (wild type canonical) (SEQ ID NO: 12) 1 = C3HHTKICLRGSQLV (wild-type altered to non- canonical) (SEQ ID NO: 13) 2HTKG CLRGSQLV (SEQ ID NO: 14) 3 HTKA CLRGSQLV (SEQ ID NO: 15) 4 HTKVCLRGSQLV (SEQ ID NO: 16) 5 HTKL CLRGSQLV (SEQ ID NO: 17) 6 HTKS CLRGSQLV(SEQ ID NO: 18) 7 HTKN CLRGSQLV (SEQ ID NO: 19) 8 HTKK CLRGSQLV (SEQ IDNO: 20) 9 HTKR CLRGSQLV (SEQ ID NO: 21) 10 HTKIGG CLRGSQLV (SEQ ID NO:22) 11 HTKIC GLRGSQLV (SEQ ID NO: 23) 12 HTKIC GGLRGSQLV (SEQ ID NO: 24)13 HTKIG C GLRGSQLV (SEQ ID NO: 25) 14 HTKIG C GGLRGSQLV (SEQ ID NO: 26)15 H LKGN CLRGSQLV (SEQ ID NO: 27) 16 H LKGN C PAGSQLV (SEQ ID NO: 28)17 H SEGG CLRGSQLV (SEQ ID NO: 29) 18 H SEGG C PGGSQLV (SEQ ID NO: 30)19 H SSSN CLRGSQLV (SEQ ID NO: 31) 20 H SSSN C TIGSQLV (SEQ ID NO: 32)

TABLE 2 1 HTKIC GGGLRGSQLV (SEQ ID NO: 33) 2 HTKIG C GGGLRGSQLV (SEQ IDNO: 34) 3 HTKIGG CLRGSQLV (SEQ ID NO: 35) 4 HTKIGG C GLRGSQLV (SEQ IDNO: 36) 5 HTKIGG C GGLRGSQLV (SEQ ID NO: 37) 6 HTKR C GLRGSQLV (SEQ IDNO: 38) 7 HTKR C GGLRGSQLV (SEQ ID NO: 39) 8 HTKR C GGGLRGSQLV (SEQ IDNO: 40) 9 HTKRG CLRGSQLV (SEQ ID NO: 41) 10 HTKRG C GLRGSQLV (SEQ ID NO:42) 11 HTKRG C GGLRGSQLV (SEQ ID NO: 43) 12 HTKRG C GGGLRGSQLV (SEQ IDNO: 44) 13 HTKRGG CLRGSQLV (SEQ ID NO: 45) 14 HTKRGG C GLRGSQLV (SEQ IDNO: 46) 15 HTKRGG C GGLRGSQLV (SEQ ID NO: 47) 16 H LKGN C GLRGSQLV (SEQID NO: 48) 17 H LKGN C GGLRGSQLV (SEQ ID NO: 49) 18 H LKGN C GGGLRGSQLV(SEQ ID NO: 50) 19 H KER C GLRGSQLV (SEQ ID NO: 51) 20 HTRR C GLRGSQLV(SEQ ID NO: 52) 21 H AQR C GLRGSQLV (SEQ ID NO: 53) 22 H KKFY C GLRGSQLV(SEQ ID NO: 54) 23 H KKHY C GLRGSQLV (SEQ ID NO: 55) 24 H KKYT CGLRGSQLV (SEQ ID NO: 56) 25 H KKYY C GLRGSQLV (SEQ ID NO: 57) 26 H KQYYC GLRGSQLV (SEQ ID NO: 58) 27 H LLKK C GLRGSQLV (SEQ ID NO: 59) 28 HQKFP C GLRGSQLV (SEQ ID NO: 60) 29 H QKKL C GLRGSQLV (SEQ ID NO: 61) 30H QIRG C GLRGSQLV (SEQ ID NO: 62) 31 H IKRQS C GLRGSQLV (SEQ ID NO: 63)32 H IRRYT C GLRGSQLV (SEQ ID NO: 64) 33 H ISSKK C GLRGSQLV (SEQ ID NO:65) 34 H KIQKA C GLRGSQLV (SEQ ID NO: 66) 35 H KRIYT C GLRGSQLV (SEQ IDNO: 67) 36 H LKGQN C GLRGSQLV (SEQ ID NO: 68) 37 H LKKDG C GLRGSQLV (SEQID NO: 69) 38 H LKYTP C GLRGSQLV (SEQ ID NO: 70) 39 HTKR C GRGSQLV (SEQID NO: 71) 40 HTKIG C GGRGSQLV (SEQ ID NO: 72) 41 H LKGN C GRGSQLV (SEQID NO: 73) 42 H LKGN C GGGSQLV (SEQ ID NO: 74) 43 HIRTCTGSQKP (SEQ IDNO: 75) 44 HIRTC GTGSQKP (SEQ ID NO: 76) 45 HIRTG CTGSQKP (SEQ ID NO:77) 46 HIRTG C GTGSQKP (SEQ ID NO: 78) 47 HIRR CTGSQKP (SEQ ID NO: 79)48 HIRRG CTGSQKP (SEQ ID NO: 80)

TABLE 3 wt HTKIHTGSQKP (SEQ ID NO: 81) 1a HTKICTGSQKP (SEQ ID NO: 82) 2aHTKR CTGSQKP (SEQ ID NO: 83) 3a H AQR CTGSQKP (SEQ ID NO: 84) 4a HTKICGTGSQKP (SEQ ID NO: 85) 5a HTKR C GTGSQKP (SEQ ID NO: 86) 6a H AQR CGTGSQKP (SEQ ID NO: 87)

TABLE 4 wt HTKIHLRGSQLV (SEQ ID NO: 88)  7a H AQR C GG (SEQ ID NO: 89) 8a H AQR C GGG (SEQ ID NO: 90)  9a HTKIC GGG (SEQ ID NO: 91) 10a HTKR CGGG (SEQ ID NO: 92) 11a H AQR C G (SEQ ID NO: 93)

As noted above, a ZFP can include any number of zinc finger bindingdomains, for example at least 3 zinc fingers. Furthermore, one, morethan one, or all of the zinc fingers may be non-canonical zinc fingersas described herein.

In certain embodiments, the C-terminal-most finger of a multi-fingerzinc finger protein comprises a canonical zinc finger. In otherembodiments, the C-terminal-most finger of a multi-finger zinc fingerprotein comprises a CCHC finger as described herein, for example a CCHCfinger comprising one or more amino acid insertions C-terminal to theC-terminal-most zinc-coordinating Cys residue. See Examples 1-5describing 4-fingered zinc finger proteins in which finger 2 (F2) and/orfinger 4 (F4) are non-canonical zinc fingers as described herein.

Zinc finger binding domains can be engineered to bind to a sequence ofchoice. See, for example, Beerli et al. (2002) Nature Biotechnol.20:135-141; Pabo et al. (2001) Ann. Rev. Biochem. 70:313-340; Isalan etal. (2001) Nature Biotechnol. 19:656-660; Segal et al. (2001) Curr.Opin. Biotechnol. 12:632-637; Choo et al. (2000) Curr. Opin. Struct.Biol. 10:411-416. An engineered zinc finger binding domain can have anovel binding specificity, compared to a naturally-occurring zinc fingerprotein. Engineering methods include, but are not limited to, rationaldesign and various types of selection (e.g., methods in which aplurality of different zinc finger sequences are screened against asingle target nucleotide sequence). Rational design includes, forexample, using databases comprising triplet (or quadruplet) nucleotidesequences and individual zinc finger amino acid sequences, in which eachtriplet or quadruplet nucleotide sequence is associated with one or moreamino acid sequences of zinc fingers which bind the particular tripletor quadruplet sequence. See, for example, co-owned U.S. Pat. Nos.6,453,242 and 6,534,261. Additional design methods are disclosed, forexample, in U.S. Pat. Nos. 6,746,838; 6,785,613; 6,866,997; and7,030,215. Enhancement of binding specificity for zinc finger bindingdomains has been described, for example, in co-owned U.S. Pat. No.6,794,136.

Exemplary selection methods, including phage display and two-hybridsystems, are disclosed in U.S. Pat. Nos. 5,789,538; 5,925,523;6,007,988; 6,013,453; 6,410,248; 6,140,466; 6,200,759; and 6,242,568; aswell as WO 98/37186; WO 98/53057; WO 00/27878; WO 01/88197 and GB2,338,237.

Since an individual zinc finger binds to a three-nucleotide (i.e.,triplet) sequence (or a four-nucleotide sequence which can overlap, byone nucleotide, with the four-nucleotide binding site of an adjacentzinc finger), the length of a sequence to which a zinc finger bindingdomain is engineered to bind (e.g., a target sequence) will determinethe number of zinc fingers in an engineered zinc finger binding domain.For example, for ZFPs in which the zinc finger motifs do not bind tooverlapping subsites, a six-nucleotide target sequence is bound by atwo-finger binding domain; a nine-nucleotide target sequence is bound bya three-finger binding domain, etc. Binding sites for individual zincfingers (i.e., subsites) in a target site need not be contiguous, butcan be separated by one or several nucleotides, depending on the lengthand nature of the amino acids sequences between the zinc fingers (i.e.,the inter-finger linkers) in a multi-finger binding domain. See, forexample, U.S. Pat. Nos. 6,479,626; 6,903,185 and 7,153,949 and U.S.Patent Application Publication No. 2003/0119023; the disclosures ofwhich are incorporated by reference.

In a multi-finger zinc finger binding domain, adjacent zinc fingers canbe separated by amino acid linker sequences of approximately 5 aminoacids (so-called “canonical” inter-finger linkers) or, alternatively, byone or more non-canonical linkers. See, e.g., co-owned U.S. Pat. Nos.6,453,242 and 6,534,261. For engineered zinc finger binding domainscomprising more than three fingers, insertion of longer(“non-canonical”) inter-finger linker sequences between certain of thezinc fingers may increase the affinity and/or specificity of binding bythe binding domain. See, for example, U.S. Pat. No. 6,479,626 and U.S.Patent Application Publication No. 2003/0119023; the disclosures ofwhich are incorporated by reference. Accordingly, multi-finger zincfinger binding domains can also be characterized with respect to thepresence and location of non-canonical inter-finger linkers. Use oflonger inter-finger linkers can also facilitate the binding of a zincfinger protein to target sites comprising non-contiguous nucleotides. Asa result, one or more subsites, in a target site for a zinc fingerbinding domain, can be separated from each other by 1, 2, 3, 4, 5 ormore nucleotides. To provide but one example, a four-finger bindingdomain can bind to a 13-nucleotide target site comprising, in sequence,two contiguous 3-nucleotide subsites, an intervening nucleotide, and twocontiguous triplet subsites.

A target subsite is a nucleotide sequence (generally 3 or 4 nucleotides)that is bound by a single zinc finger. However, it is not necessary fora target site to be a multiple of three nucleotides. For example, incases in which cross-strand interactions occur (see, e.g., U.S. Pat.Nos. 6,453,242 and 6,794,136), one or more of the individual zincfingers of a multi-finger binding domain can bind to overlappingquadruplet subsites. See also U.S. Pat. Nos. 6,746,838 and 6,866,997. Toprovide but one example, a three-finger binding domain can bind to a10-nucleotide target site comprising three overlapping 4-nucleotidesubsites.

Selection of a sequence in cellular chromatin for binding by a zincfinger domain (e.g., a target site) can be accomplished, for example,according to the methods disclosed in co-owned U.S. Pat. No. 6,453,242(Sep. 17, 2002), which also discloses methods for designing ZFPs to bindto a selected sequence. It will be clear to those skilled in the artthat simple visual inspection of a nucleotide sequence can also be usedfor selection of a target site. Accordingly, any means for target siteselection can be used in the methods described herein.

Multi-finger zinc finger proteins can be constructed by joiningindividual zinc fingers obtained, for example, by design or selection.Alternatively, binding modules consisting of two zinc fingers can bejoined to one another, using either canonical or longer, non-canonicalinter-finger linkers (see above) to generate four- and six-fingerproteins. Such two finger modules can be obtained, for example, byselecting for two adjacent fingers, which bind a particularsix-nucleotide target sequence, in the context of a multi-finger protein(generally three fingers). See, for example, WO 98/53057 and U.S. PatentApplication Publication No. 2003/0119023; the disclosures of which areincorporated by reference. Alternatively, two-finger modules can beconstructed by assembly of individual zinc fingers.

Thus, the zinc finger domains described herein can be used individuallyor in various combinations to construct multi-finger zinc fingerproteins that bind to any target site.

Distance between sequences (e.g., target sites) refers to the number ofnucleotides or nucleotide pairs intervening between two sequences, asmeasured from the edges of the sequences nearest each other.

In embodiments using ZFNs, for example in which cleavage depends on thebinding of two zinc finger domain/cleavage half-domain fusion moleculesto separate target sites, the two target sites can be on opposite DNAstrands. In other embodiments, both target sites are on the same DNAstrand. See, for example, WO 2005/084190; the disclosure of which isincorporated by reference.

Polynucleotides encoding zinc fingers or zinc finger proteins are alsowithin the scope of the present disclosure. These polynucleotides can beconstructed using standard techniques and inserted into a vector, andthe vector can be introduced into a cell (see below for additionaldisclosure regarding vectors and methods for introducing polynucleotidesinto cells) such that the encoded protein is expressed in the cell.

Fusion Proteins

Fusion proteins comprising one or more non-canonical zinc fingercomponents described herein are also provided.

Fusion molecules are constructed by methods of cloning and biochemicalconjugation that are well known to those of skill in the art. Fusionmolecules comprise a CCHC-containing ZFP and, for example, a cleavagedomain, a cleavage half-domain, a transcriptional activation domain, atranscriptional repression domain, a component of a chromatin remodelingcomplex, an insulator domain, a functional fragment of any of thesedomains; and/or any combinations of two or more functional domains orfragments thereof.

In certain embodiments, fusion molecules comprise a modified plant zincfinger protein and at least two functional domains (e.g., an insulatordomain or a methyl binding protein domain and, additionally, atranscriptional activation or repression domain).

Fusion molecules also optionally comprise a nuclear localization signal(such as, for example, that from the SV40 T-antigen or the maizeOpaque-2 NLS) and an epitope tag (such as, for example, FLAG orhemagglutinin). Fusion proteins (and nucleic acids encoding them) aredesigned such that the translational reading frame is preserved amongthe components of the fusion.

Methods for design and construction of fusion proteins (andpolynucleotides encoding same) are known to those of skill in the art.For example, methods for the design and construction of fusion proteincomprising zinc finger proteins (and polynucleotides encoding same) aredescribed in co-owned U.S. Pat. Nos. 6,453,242 and 6,534,261.

Polynucleotides encoding such fusion proteins are also within the scopeof the present disclosure. These polynucleotides can be constructedusing standard techniques and inserted into a vector and the vector canbe introduced into a cell (see below for additional disclosure regardingvectors and methods for introducing polynucleotides into cells).

An exemplary functional domain for fusing with a ZFP DNA-binding domain,to be used for repressing gene expression, is a KRAB repression domainfrom the human KOX-1 protein (see, e.g., Thiesen et al., New Biologist2, 363-374 (1990); Margolin et al., Proc. Natl. Acad. Sci. USA 91,4509-4513 (1994); Pengue et al., Nucl. Acids Res. 22:2908-2914 (1994);Witzgall et al., Proc. Natl. Acad. Sci. USA 91, 4514-4518 (1994). TheKOX domain is also suitable for use as a repression domain. Anothersuitable repression domain is methyl binding domain protein 2B (MBD-2B)(see, also Hendrich et al. (1999) Mamm Genome 10:906-912 for descriptionof MBD proteins). Another useful repression domain is that associatedwith the v-ErbA protein. See, for example, Damm, et al. (1989) Nature339:593-597; Evans (1989) Int. J. Cancer Suppl. 4:26-28; Pain et al.(1990) New Biol. 2:284-294; Sap et al. (1989) Nature 340:242-244; Zenkeet al. (1988) Cell 52:107-119; and Zenke et al. (1990) Cell61:1035-1049. Additional exemplary repression domains include, but arenot limited to, thyroid hormone receptor (TR), SID, MBD1, MBD2, MBD3,MBD4, MBD-like proteins, members of the DNMT family (e.g., DNMT1,DNMT3A, DNMT3B), Rb, MeCP1 and MeCP2. See, for example, Zhang et al.(2000) Ann Rev Physiol 62:439-466; Bird et al. (1999) Cell 99:451-454;Tyler et al. (1999) Cell 99:443-446; Knoepfler et al. (1999) Cell99:447-450; and Robertson et al. (2000) Nature Genet. 25:338-342.Additional exemplary repression domains include, but are not limited to,ROM2 and AtHD2A. See, for example, Chem et al. (1996) Plant Cell8:305-321; and Wu et al. (2000) Plant J. 22:19-27.

Suitable domains for achieving activation include the HSV VP16activation domain (see, e.g., Hagmann et al., J. Virol. 71, 5952-5962(1997)) nuclear hormone receptors (see, e.g., Torchia et al., Curr.Opin. Cell. Biol. 10:373-383 (1998)); the p65 subunit of nuclear factorkappa B (Bitko & Barik, J. Virol. 72:5610-5618 (1998) and Doyle & Hunt,Neuroreport 8:2937-2942 (1997)); Liu et al., Cancer Gene Ther. 5:3-28(1998)), or artificial chimeric functional domains such as VP64 (Seifpalet al., EMBO J. 11, 4961-4968 (1992)).

Additional exemplary activation domains include, but are not limited to,p300, CBP, PCAF, SRC1 PvALF, and ERF-2. See, for example, Robyr et al.(2000) Mol. Endocrinol. 14:329-347; Collingwood et al. (1999) J. Mol.Endocrinol. 23:255-275; Leo et al. (2000) Gene 245:1-11;Manteuffel-Cymborowska (1999) Acta Biochim. Pol. 46:77-89; McKenna etal. (1999) J. Steroid Biochem. Mol. Biol. 69:3-12; Malik et al. (2000)Trends Biochem. Sci. 25:277-283; and Lemon et al. (1999) Curr. Opin.Genet. Dev. 9:499-504. Additional exemplary activation domains include,but are not limited to, OsGAI, HALF-1, C1, AP1, ARF-5, -6, -7, and -8,CPRF1, CPRF4, MYC-RP/GP, and TRAB1. See, for example, Ogawa et al.(2000) Gene 245:21-29; Okanami et al. (1996) Genes Cells 1:87-99; Goffet al. (1991) Genes Dev. 5:298-309; Cho et al. (1999) Plant Mol. Biol.40:419-429; Ulmason et al. (1999) Proc. Natl. Acad. Sci. USA96:5844-5849; Sprenger-Haussels et al. (2000) Plant J. 22:1-8; Gong etal. (1999) Plant Mol. Biol. 41:33-44; and Hobo et al. (1999) Proc. Natl.Acad. Sci. USA 96:15,348-15,353.

Additional functional domains are disclosed, for example, in co-ownedU.S. Pat. No. 6,933,113. Further, insulator domains, chromatinremodeling proteins such as ISWI-containing domains, and methyl bindingdomain proteins suitable for use in fusion molecules are described, forexample, in co-owned International Publications WO 01/83793 and WO02/26960.

In other embodiments, the fusion protein is a zinc finger nuclease (ZFN)comprising one or more CCHC zinc fingers as described herein and acleavage domain (or cleavage half-domain). The zinc fingers can beengineered to recognize a target sequence in any genomic region ofchoice and, when introduced into a cell, will result in binding of thefusion protein(s) to its (their) binding site(s) and cleavage within ornear said genomic region. Such cleavage can result in alteration of thenucleotide sequence of the genomic region (e.g., mutation) followingnon-homologous end joining. Alternatively, if an exogenouspolynucleotide containing sequences homologous to the genomic region isalso present in such a cell, homologous recombination occurs at a highrate between the genomic region and the exogenous polynucleotide,following targeted cleavage by the ZFNs. Homologous recombination canresult in targeted sequence replacement or targeted integration ofexogenous sequences, depending on the nucleotide sequence of theexogenous polynucleotide.

The non-canonical zinc fingers described herein provide improvedcleavage function when incorporated into ZFNs. As described in theExamples, 4-fingered ZFNs containing at least one CCHC finger asdescribed herein cleave at least as well as nucleases containingexclusively CCHH fingers. In certain embodiments, when the C-terminalfinger comprises a non-canonical CCHC zinc finger, the residues betweenthe third and fourth zinc-coordinating residues (i.e., between theC-terminal His and Cys residues) are different than those present in acanonical CCHH zinc finger, and one or more glycine residues (e.g., 1,2, 3, 4, 5 or more) are inserted after the C-terminal Cys residue.

The cleavage domain portion of the ZFNs disclosed herein can be obtainedfrom any endonuclease or exonuclease. Exemplary endonucleases from whicha cleavage domain can be derived include, but are not limited to,restriction endonucleases and homing endonucleases. See, for example,2002-2003 Catalogue, New England Biolabs, Beverly, MA; and Belfort etal. (1997) Nucleic Acids Res. 25:3379-3388. Additional enzymes whichcleave DNA are known (e.g., S1 Nuclease; mung bean nuclease; pancreaticDNase I; micrococcal nuclease; yeast HO endonuclease; see also Linn etal. (eds.) Nucleases, Cold Spring Harbor Laboratory Press, 1993). One ormore of these enzymes (or functional fragments thereof) can be used as asource of cleavage domains and cleavage half-domains.

Similarly, a cleavage half-domain can be derived from any nuclease orportion thereof, as set forth above, providing the cleavage half-domainrequires dimerization for cleavage activity. In general, two fusionproteins are required for targeted cleavage of genomic DNA if the fusionproteins comprise cleavage half-domains. Alternatively, a single proteincomprising two cleavage half-domains can be used. The two cleavagehalf-domains can be derived from the same endonuclease, or each cleavagehalf-domain can be derived from a different endonuclease. In addition,the target sites for the two fusion proteins are disposed, with respectto each other, such that binding of the two fusion proteins to theirrespective target sites places the cleavage half-domains in a spatialorientation to each other that allows the cleavage half-domains to forma functional cleavage domain, e.g., by dimerizing. Thus, in certainembodiments, the near edges of the target sites are separated by 5-8nucleotide pairs or by 15-18 nucleotide pairs. In additionalembodiments, the target sites are within ten nucleotide pairs of eachother. However any integral number of nucleotides or nucleotide pairscan intervene between two target sites (e.g., from 2 to 50 nucleotidesor more). In general, the point of cleavage lies between the targetsites.

Restriction endonucleases (restriction enzymes) are present in manyspecies and are capable of sequence-specific binding to DNA (at arecognition site), and cleaving DNA at or near the site of binding.Certain restriction enzymes (e.g., Type IIS) cleave DNA at sites removedfrom the recognition site and have separable binding and cleavagedomains. For example, the Type IIS enzyme Fok I catalyzesdouble-stranded cleavage of DNA, at 9 nucleotides from its recognitionsite on one strand and 13 nucleotides from its recognition site on theother. See, for example, U.S. Pat. Nos. 5,356,802; 5,436,150 and5,487,994; as well as Li et al. (1992) Proc. Natl. Acad. Sci. USA89:4275-4279; Li et al. (1993) Proc. Natl. Acad. Sci. USA 90:2764-2768;Kim et al. (1994a) Proc. Natl. Acad. Sci. USA 91:883-887; Kim et al.(1994b) J. Biol. Chem. 269:31,978-31,982. Thus, in one embodiment,fusion proteins comprise the cleavage domain (or cleavage half-domain)from at least one Type IIS restriction enzyme and one or more zincfinger binding domains, which may or may not be engineered.

An exemplary Type IIS restriction enzyme, whose cleavage domain isseparable from the binding domain, is Fok I. This particular enzyme isactive as a dimer. Bitinaite et al. (1998) Proc. Natl. Acad. Sci. USA95: 10,570-10,575. Accordingly, for the purposes of the presentdisclosure, the portion of the Fok I enzyme used in the disclosed fusionproteins is considered a cleavage half-domain. Thus, for targeteddouble-stranded cleavage and/or targeted replacement of cellularsequences using ZFNs comprising zinc finger-Fok I fusions, two fusionproteins, each comprising a FokI cleavage half-domain, can be used toreconstitute a catalytically active cleavage domain. Alternatively, asingle polypeptide molecule containing a zinc finger binding domain andtwo Fok I cleavage half-domains can also be used. Parameters fortargeted cleavage and targeted sequence alteration using zinc finger-FokI fusions are provided elsewhere in this disclosure and, for example, inUS Patent Application Publication No. 2005/0064474; the disclosure ofwhich is incorporated by reference.

In additional embodiments, a FokI cleavage half-domain may include oneor more mutations at any amino acid residue which affects dimerization.Such mutations can be useful for preventing one of a pair of ZFP/FokIfusions from undergoing homodimerization which can lead to cleavage atundesired sequences. For example, amino acid residues at positions 446,447, 479, 483, 484, 486, 487, 490, 491, 496, 498, 499, 500, 531, 534,537, and 538 of Fok1 are all close enough to the dimerization interfaceto influence dimerization. Accordingly, amino acid sequence alterationsat one or more of the aforementioned positions can be used to alter thedimerization properties of the cleavage half-domain. Such changes can beintroduced, for example, by constructing a library containing (orencoding) different amino acid residues at these positions and selectingvariants with the desired properties, or by rationally designingindividual mutants. In addition to preventing homodimerization, it isalso possible that some of these mutations may increase the cleavageefficiency, compared to that obtained with two wild-type cleavagehalf-domains.

Thus, for targeted cleavage using a pair of ZFP/FokI fusions, one orboth of the fusion proteins can comprise one or more amino acidalterations that inhibit self-dimerization, but allow heterodimerizationof the two fusion proteins to occur such that cleavage occurs at thedesired target site. In certain embodiments, alterations are present inboth fusion proteins, and the alterations have additive effects; i.e.,homodimerization of either fusion, leading to aberrant cleavage, isminimized or abolished, while heterodimerization of the two fusionproteins is facilitated compared to that obtained with wild-typecleavage half-domains.

In certain embodiments, the cleavage domain comprises two cleavagehalf-domains, both of which are part of a single polypeptide comprisinga binding domain, a first cleavage half-domain and a second cleavagehalf-domain. The cleavage half-domains can have the same amino acidsequence or different amino acid sequences, so long as they function tocleave the DNA.

Cleavage half-domains may also be provided in separate molecules. Forexample, two fusion polypeptides may be expressed in a cell, whereineach polypeptide comprises a binding domain and a cleavage half-domain.The cleavage half-domains can have the same amino acid sequence ordifferent amino acid sequences, so long as they function to cleave theDNA. Further, the binding domains bind to target sequences which aretypically disposed in such a way that, upon binding of the fusionpolypeptides, the two cleavage half-domains are presented in a spatialorientation to each other that allows reconstitution of a cleavagedomain (e.g., by dimerization of the half-domains), thereby positioningthe half-domains relative to each other to form a functional cleavagedomain, resulting in cleavage of cellular chromatin in a region ofinterest. Generally, cleavage by the reconstituted cleavage domainoccurs at a site located between the two target sequences. One or bothof the proteins can be engineered to bind to its target site.

Expression of two fusion proteins in a cell can result from delivery ofthe two proteins to the cell; delivery of one protein and one nucleicacid encoding one of the proteins to the cell; delivery of two nucleicacids, each encoding one of the proteins, to the cell; or by delivery ofa single nucleic acid, encoding both proteins, to the cell. Inadditional embodiments, a fusion protein comprises a single polypeptidechain comprising two cleavage half domains and a zinc finger bindingdomain. In this case, a single fusion protein is expressed in a celland, without wishing to be bound by theory, is believed to cleave DNA asa result of formation of an intramolecular dimer of the cleavagehalf-domains.

In certain embodiments, the components of a ZFN are arranged such thatthe zinc finger domain is nearest the amino terminus of the fusionprotein, and the cleavage half-domain is nearest the carboxy-terminus.This mirrors the relative orientation of the cleavage domain innaturally-occurring dimerizing cleavage domains such as those derivedfrom the Fok I enzyme, in which the DNA-binding domain is nearest theamino terminus and the cleavage half-domain is nearest the carboxyterminus. In these embodiments, dimerization of the cleavagehalf-domains to form a functional nuclease is brought about by bindingof the fusion proteins to sites on opposite DNA strands, with the 5′ends of the binding sites being proximal to each other.

In this orientation, the C-terminal-most zinc finger is proximal to theFokI cleavage half-domain. It has previously been determined thatnon-canonical zinc finger proteins bind their DNA targets mostefficiently when a CCHC-type zinc finger is present as theC-terminal-most finger. It is therefore possible that the presence ofpreviously-described CCHC-type zinc fingers in proximity to the FokIcleavage half-domain inhibited its function. If this is the case, thepresently-disclosed optimized CCHC zinc fingers apparently do notexhibit this postulated inhibitory activity.

In additional embodiments, the components of the fusion proteins (e.g.,ZFP-Fok I fusions) are arranged such that the cleavage half-domain isnearest the amino terminus of the fusion protein, and the zinc fingerdomain is nearest the carboxy-terminus. In these embodiments,dimerization of the cleavage half-domains to form a functional nucleaseis brought about by binding of the fusion proteins to sites on oppositeDNA strands, with the 3′ ends of the binding sites being proximal toeach other.

In yet additional embodiments, a first fusion protein contains thecleavage half-domain nearest the amino terminus of the fusion protein,and the zinc finger domain nearest the carboxy-terminus, and a secondfusion protein is arranged such that the zinc finger domain is nearestthe amino terminus of the fusion protein, and the cleavage half-domainis nearest the carboxy-terminus. In these embodiments, both fusionproteins bind to the same DNA strand, with the binding site of the firstfusion protein containing the zinc finger domain nearest the carboxyterminus located to the 5′ side of the binding site of the second fusionprotein containing the zinc finger domain nearest the amino terminus.See also WO 2005/084190; the disclosure of which is incorporated byreference.

The amino acid sequence between the zinc finger domain and the cleavagedomain (or cleavage half-domain) is denoted the “ZC linker.” The ZClinker is to be distinguished from the inter-finger linkers discussedabove. See, e.g., U.S. Patent Publications 20050064474A1 and20030232410, and International Patent Publication WO 2005/084190; thedisclosures of which are incorporated by reference, for details onobtaining ZC linkers that optimize cleavage.

Expression Vectors

A nucleic acid encoding one or more ZFPs or ZFP fusion proteins (e.g.,ZFNs) can be cloned into a vector for transformation into prokaryotic oreukaryotic cells for replication and/or expression. Vectors can beprokaryotic or eukaryotic vectors, including but not limited to,plasmids, shuttle vectors, insect vectors, binary vectors (see, e.g.,U.S. Pat. No. 4,940,838; Horsch et al (1984) Science 233:496-498, andFraley et al (1983) Proc. Nat'l. Acad. Sci. USA 80:4803) and the like. Anucleic acid encoding a ZFP can also be cloned into an expressionvector, for administration to a plant cell.

To express the fusion proteins, sequences encoding the ZFPs or ZFPfusions are typically subcloned into an expression vector that containsa promoter to direct transcription. Suitable bacterial and eukaryoticpromoters are well known in the art and described, e.g., in Sambrook etal., Molecular Cloning, A Laboratory Manual (2nd ed. 1989; 3^(rd) ed.,2001); Kriegler, Gene Transfer and Expression: A Laboratory Manual(1990); and Current Protocols in Molecular Biology (Ausubel et al.,supra. Bacterial expression systems for expressing the ZFP are availablein, e.g., E. coli, Bacillus sp., and Salmonella (Palva et al., Gene22:229-235 (1983)). Kits for such expression systems are commerciallyavailable. Eukaryotic expression systems for mammalian cells, yeast, andinsect cells are well known by those of skill in the art and are alsocommercially available.

The promoter used to direct expression of a ZFP-encoding nucleic aciddepends on the particular application. For example, a strongconstitutive promoter suited to the host cell is typically used forexpression and purification of ZFPs.

In contrast, when a ZFP is administered in vivo for plant generegulation (see, “Nucleic Acid Delivery to Plant Cells” section below),either a constitutive or an inducible promoter is used, depending on theparticular use of the ZFP. Non-limiting examples of plant promotersinclude promoter sequences derived from A. thaliana ubiguitin-3 (ubi-3)(Callis, et al., 1990, J. Biol. Chem. 265-12486-12493); A. tumifaciensmannopine synthase (Δmas) (Petolino et al., U.S. Pat. No. 6,730,824);and/or Cassava Vein Mosaic Virus (CsVMV) (Verdaguer et al., 1996, PlantMolecular Biology 31:1129-1139). See, also, Examples.

In addition to the promoter, the expression vector typically contains atranscription unit or expression cassette that contains all theadditional elements required for the expression of the nucleic acid inhost cells, either prokaryotic or eukaryotic. A typical expressioncassette thus contains a promoter operably linked, e.g., to a nucleicacid sequence encoding the ZFP, and signals required, e.g., forefficient polyadenylation of the transcript, transcriptionaltermination, ribosome binding sites, or translation termination.Additional elements of the cassette may include, e.g., enhancers, andheterologous splicing signals.

The particular expression vector used to transport the geneticinformation into the cell is selected with regard to the intended use ofthe ZFP, e.g., expression in plants, animals, bacteria, fungus,protozoa, etc. (see expression vectors described below). Standardbacterial and animal expression vectors are known in the art and aredescribed in detail, for example, U.S. Patent Publication 20050064474A1and International Patent Publications WO05/084190, WO05/014791 andWO03/080809; the disclosures of which are incorporated by reference.

Standard transfection methods can be used to produce bacterial,mammalian, yeast or insect cell lines that express large quantities ofprotein, which can then be purified using standard techniques (see,e.g., Colley et al., J. Biol. Chem. 264:17619-17622 (1989); Guide toProtein Purification, in Methods in Enzymology, vol. 182 (Deutscher,ed., 1990)). Transformation of eukaryotic and prokaryotic cells areperformed according to standard techniques (see, e.g., Morrison, J.Bact. 132:349-351 (1977); Clark-Curtiss & Curtiss, Methods in Enzymology101:347-362 (Wu et al., eds., 1983).

Any of the well known procedures for introducing foreign nucleotidesequences into such host cells may be used. These include the use ofcalcium phosphate transfection, polybrene, protoplast fusion,electroporation, ultrasonic methods (e.g., sonoporation), liposomes,microinjection, naked DNA, plasmid vectors, viral vectors, both episomaland integrative, and any of the other well known methods for introducingcloned genomic DNA, cDNA, synthetic DNA or other foreign geneticmaterial into a host cell (see, e.g., Sambrook et al., supra). It isonly necessary that the particular genetic engineering procedure used becapable of successfully introducing at least one gene into the host cellcapable of expressing the protein of choice.

Nucleic Acid Delivery to Plant Cells

As noted above, DNA constructs may be introduced into (e.g., into thegenome of) a desired plant host by a variety of conventional techniques.For reviews of such techniques see, for example, Weissbach & WeissbachMethods for Plant Molecular Biology (1988, Academic Press, N.Y.) SectionVIII, pp. 421-463; and Grierson & Corey, Plant Molecular Biology (1988,2d Ed.), Blackie, London, Ch. 7-9.

For example, the DNA construct may be introduced into a plant cell usingtechniques such as electroporation and microinjection of plant cellprotoplasts, or the DNA constructs can be introduced directly to planttissue using biolistic methods, such as DNA particle bombardment (see,e.g., Klein et al (1987) Nature 327:70-73). Alternatively, the DNAconstructs may be combined with suitable T-DNA flanking regions andintroduced into a conventional Agrobacterium tumefaciens host vector.Agrobacterium tumefaciens-mediated transformation techniques, includingdisarming and use of binary vectors, are well described in thescientific literature. See, for example Horsch et al (1984) Science233:496-498, and Fraley et al (1983) Proc. Nat'l. Acad. Sci. USA80:4803.

In addition, gene transfer may be achieved using non-Agrobacteriumbacteria or viruses such as Rhizobium sp. NGR234, Sinorhizoboiummeliloti, Mesorhizobium loti, potato virus X, cauliflower mosaic virusand cassava vein mosaic virus and/or tobacco mosaic virus, See, e.g.,Chung et al. (2006) Trends Plant Sci. 11(1):1-4.

The virulence functions of the Agrobacterium tumefaciens host willdirect the insertion of the construct and adjacent marker into the plantcell DNA when the cell is infected by the bacteria using binary T DNAvector (Bevan (1984) Nuc. Acid Res. 12:8711-8721) or the co-cultivationprocedure (Horsch et al (1985) Science 227:1229-1231). Generally, theAgrobacterium transformation system is used to engineer dicotyledonousplants (Bevan et al (1982) Ann. Rev. Genet 16:357-384; Rogers et al(1986) Methods Enzymol. 118:627-641). The Agrobacterium transformationsystem may also be used to transform, as well as transfer, DNA tomonocotyledonous plants and plant cells. See U.S. Pat. No. 5,591,616;Hernalsteen et al (1984) EMBO J 3:3039-3041; Hooykass-Van Slogteren etal (1984) Nature 311:763-764; Grimsley et al (1987) Nature 325:1677-179;Boulton et al (1989) Plant Mol. Biol. 12:31-40.; and Gould et al (1991)Plant Physiol. 95:426-434.

Alternative gene transfer and transformation methods include, but arenot limited to, protoplast transformation through calcium-, polyethyleneglycol (PEG)- or electroporation-mediated uptake of naked DNA (seePaszkowski et al. (1984) EMBO J 3:2717-2722, Potrykus et al. (1985)Molec. Gen. Genet. 199:169-177; Fromm et al. (1985) Proc. Nat. Acad.Sci. USA 82:5824-5828; and Shimamoto (1989) Nature 338:274-276) andelectroporation of plant tissues (D'Halluin et al. (1992) Plant Cell4:1495-1505). Additional methods for plant cell transformation includemicroinjection, silicon carbide mediated DNA uptake (Kaeppler et al.(1990) Plant Cell Reporter 9:415-418), and microprojectile bombardment(see Klein et al. (1988) Proc. Nat. Acad. Sci. USA 85:4305-4309; andGordon-Kamm et al. (1990) Plant Cell 2:603-618).

The disclosed methods and compositions can be used to insert exogenoussequences into a predetermined location in a plant cell genome. This isuseful inasmuch as expression of an introduced transgene into a plantgenome depends critically on its integration site. Accordingly, genesencoding, e.g., nutrients, antibiotics or therapeutic molecules can beinserted, by targeted recombination, into regions of a plant genomefavorable to their expression.

Transformed plant cells which are produced by any of the abovetransformation techniques can be cultured to regenerate a whole plantwhich possesses the transformed genotype and thus the desired phenotype.Such regeneration techniques rely on manipulation of certainphytohormones in a tissue culture growth medium, typically relying on abiocide and/or herbicide marker which has been introduced together withthe desired nucleotide sequences. Plant regeneration from culturedprotoplasts is described in Evans, et al., “Protoplasts Isolation andCulture” in Handbook of Plant Cell Culture, pp. 124-176, MacmillianPublishing Company, New York, 1983; and Binding, Regeneration of Plants,Plant Protoplasts, pp. 21-73, CRC Press, Boca Raton, 1985. Regenerationcan also be obtained from plant callus, explants, organs, pollens,embryos or parts thereof. Such regeneration techniques are describedgenerally in Klee et al (1987) Ann. Rev. of Plant Phys. 38:467-486.

Nucleic acids introduced into a plant cell can be used to confer desiredtraits on essentially any plant. A wide variety of plants and plant cellsystems may be engineered for the desired physiological and agronomiccharacteristics described herein using the nucleic acid constructs ofthe present disclosure and the various transformation methods mentionedabove. In certain embodiments, target plants and plant cells forengineering include, but are not limited to, those monocotyledonous anddicotyledonous plants, such as crops including grain crops (e.g., wheat,maize, rice, millet, barley), fruit crops (e.g., tomato, apple, pear,strawberry, orange), forage crops (e.g., alfalfa), root vegetable crops(e.g., carrot, potato, sugar beets, yam), leafy vegetable crops (e.g.,lettuce, spinach); flowering plants (e.g., petunia, rose,chrysanthemum), conifers and pine trees (e.g., pine fir, spruce); plantsused in phytoremediation (e.g., heavy metal accumulating plants); oilcrops (e.g., sunflower, rape seed) and plants used for experimentalpurposes (e.g., Arabidopsis). Thus, the disclosed methods andcompositions have use over a broad range of plants, including, but notlimited to, species from the genera Asparagus, Avena, Brassica, Citrus,Citrullus, Capsicum, Cucurbita, Daucus, Glycine, Gossypium, Hordeum,Lactuca, Lycopersicon, Malus, Manihot, Nicotiana, Oryza, Persea, Pisum,Pyrus, Prunus, Raphanus, Secale, Solanum, Sorghum, Triticum, Vitis,Vigna, and Zea.

One of skill in the art will recognize that after the expressioncassette is stably incorporated in transgenic plants and confirmed to beoperable, it can be introduced into other plants by sexual crossing. Anyof a number of standard breeding techniques can be used, depending uponthe species to be crossed.

A transformed plant cell, callus, tissue or plant may be identified andisolated by selecting or screening the engineered plant material fortraits encoded by the marker genes present on the transforming DNA. Forinstance, selection may be performed by growing the engineered plantmaterial on media containing an inhibitory amount of the antibiotic orherbicide to which the transforming gene construct confers resistance.Further, transformed plants and plant cells may also be identified byscreening for the activities of any visible marker genes (e.g., theβ-glucuronidase, luciferase, B or C1 genes) that may be present on therecombinant nucleic acid constructs. Such selection and screeningmethodologies are well known to those skilled in the art.

Physical and biochemical methods also may be used to identify plant orplant cell transformants containing inserted gene constructs. Thesemethods include but are not limited to: 1) Southern analysis or PCRamplification for detecting and determining the structure of therecombinant DNA insert; 2) Northern blot, S1 RNase protection,primer-extension or reverse transcriptase-PCR amplification fordetecting and examining RNA transcripts of the gene constructs; 3)enzymatic assays for detecting enzyme or ribozyme activity, where suchgene products are encoded by the gene construct; 4) protein gelelectrophoresis, Western blot techniques, immunoprecipitation, orenzyme-linked immunoassays, where the gene construct products areproteins. Additional techniques, such as in situ hybridization, enzymestaining, and immunostaining, also may be used to detect the presence orexpression of the recombinant construct in specific plant organs andtissues. The methods for doing all these assays are well known to thoseskilled in the art.

Effects of gene manipulation using the methods disclosed herein can beobserved by, for example, northern blots of the RNA (e.g., mRNA)isolated from the tissues of interest. Typically, if the amount of mRNAhas increased, it can be assumed that the corresponding endogenous geneis being expressed at a greater rate than before. Other methods ofmeasuring gene and/or CYP74B activity can be used. Different types ofenzymatic assays can be used, depending on the substrate used and themethod of detecting the increase or decrease of a reaction product orby-product. In addition, the levels of and/or CYP74B protein expressedcan be measured immunochemically, i.e., ELISA, RIA, EIA and otherantibody based assays well known to those of skill in the art, such asby electrophoretic detection assays (either with staining or westernblotting). The transgene may be selectively expressed in some tissues ofthe plant or at some developmental stages, or the transgene may beexpressed in substantially all plant tissues, substantially along itsentire life cycle. However, any combinatorial expression mode is alsoapplicable.

The present disclosure also encompasses seeds of the transgenic plantsdescribed above wherein the seed has the transgene or gene construct.The present disclosure further encompasses the progeny, clones, celllines or cells of the transgenic plants described above wherein saidprogeny, clone, cell line or cell has the transgene or gene construct.

ZFPs and expression vectors encoding ZFPs can be administered directlyto the plant for targeted cleavage and/or recombination.

Administration of effective amounts is by any of the routes normallyused for introducing ZFP into ultimate contact with the plant cell to betreated. The ZFPs are administered in any suitable manner. Suitablemethods of administering such compositions are available and well knownto those of skill in the art, and, although more than one route can beused to administer a particular composition, a particular route canoften provide a more immediate and more effective reaction than anotherroute.

Carriers may also be used and are determined in part by the particularcomposition being administered, as well as by the particular method usedto administer the composition. Accordingly, there is a wide variety ofsuitable formulations of pharmaceutical compositions that are available(see, e.g., Remington's Pharmaceutical Sciences, 17^(th) ed. 1985)).

Applications

Zinc finger proteins comprising one or more non-canonical zinc fingersas described herein are useful for all genome regulation and editingapplications for which canonical C2H2 ZFPs are currently used, includingbut not limited to: gene activation; gene repression; genome editing(cleavage, targeted insertion, replacement or deletion); and epigenomeediting (via the targeting of covalent modifications of histones or ofDNA).

ZFNs comprising non-canonical zinc fingers as disclosed herein can beused to cleave DNA at a region of interest in cellular chromatin (e.g.,at a desired or predetermined site in a genome, for example, in a gene,either mutant or wild-type). For such targeted DNA cleavage, a zincfinger binding domain is engineered to bind a target site at or near thepredetermined cleavage site, and a fusion protein comprising theengineered zinc finger binding domain and a cleavage domain is expressedin a cell. Upon binding of the zinc finger portion of the fusion proteinto the target site, the DNA is cleaved near the target site by thecleavage domain. The exact site of cleavage can depend on the length ofthe ZC linker.

Alternatively, two ZFNs, each comprising a zinc finger binding domainand a cleavage half-domain, are expressed in a cell, and bind to targetsites which are juxtaposed in such a way that a functional cleavagedomain is reconstituted and DNA is cleaved in the vicinity of the targetsites. In one embodiment, cleavage occurs between the target sites ofthe two zinc finger binding domains. One or both of the zinc fingerbinding domains can be engineered.

For targeted cleavage using a zinc finger binding domain-cleavage domainfusion polypeptide, the binding site can encompass the cleavage site, orthe near edge of the binding site can be 1, 2, 3, 4, 5, 6, 10, 25, 50 ormore nucleotides (or any integral value between 1 and 50 nucleotides)from the cleavage site. The exact location of the binding site, withrespect to the cleavage site, will depend upon the particular cleavagedomain, and the length of the ZC linker. For methods in which two fusionpolypeptides, each comprising a zinc finger binding domain and acleavage half-domain, are used, the binding sites generally straddle thecleavage site. Thus the near edge of the first binding site can be 1, 2,3, 4, 5, 6, 10, 25 or more nucleotides (or any integral value between 1and 50 nucleotides) on one side of the cleavage site, and the near edgeof the second binding site can be 1, 2, 3, 4, 5, 6, 10, 25 or morenucleotides (or any integral value between 1 and 50 nucleotides) on theother side of the cleavage site. Methods for mapping cleavage sites invitro and in vivo are known to those of skill in the art.

Once introduced into, or expressed in, the target cell, the fusionprotein binds to the target sequence and cleaves at or near the targetsequence. The exact site of cleavage depends on the nature of thecleavage domain and/or the presence and/or nature of linker sequencesbetween the binding and cleavage domains. In cases where two ZFNs, eachcomprising a cleavage half-domain, are used, the distance between thenear edges of the binding sites can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25or more nucleotides (or any integral value between 1 and 50nucleotides). Optimal levels of cleavage can also depend on both thedistance between the binding sites of the two ZFNs (see, for example,Smith et al. (2000) Nucleic Acids Res. 28:3361-3369; Bibikova et al.(2001) Mol. Cell. Biol. 21:289-297) and the length of the ZC linker ineach ZFN. See, also, U.S. Patent Publication 20050064474A1 andInternational Patent Publications WO05/084190, WO05/014791 andWO03/080809, the disclosures of which are incorporated by reference.

Two ZFNs, each comprising a cleavage half-domain, can bind in the regionof interest in the same or opposite polarity, and their binding sites(i.e., target sites) can be separated by any number of nucleotides,e.g., from 0 to 50 nucleotide pairs or any integral value therebetween.In certain embodiments, the binding sites for two fusion proteins, eachcomprising a zinc finger binding domain and a cleavage half-domain, canbe located between 5 and 18 nucleotide pairs apart, for example, 5-8nucleotide pairs apart, or 15-18 nucleotide pairs apart, or 6 nucleotidepairs apart, or 16 nucleotide pairs apart, or within 10 nucleotide pairsof each other, as measured from the edge of each binding site nearestthe other binding site, and cleavage occurs between the binding sites.

The site at which the DNA is cleaved generally lies between the bindingsites for the two fusion proteins. Double-strand breakage of DNA oftenresults from two single-strand breaks, or “nicks,” offset by 1, 2, 3, 4,5, 6 or more nucleotides, (for example, cleavage of double-stranded DNAby native Fok I results from single-strand breaks offset by 4nucleotides). Thus, cleavage does not necessarily occur at exactlyopposite sites on each DNA strand. In addition, the structure of thefusion proteins and the distance between the target sites can influencewhether cleavage occurs adjacent a single nucleotide pair, or whethercleavage occurs at several sites. However, for many applications,including targeted recombination and targeted mutagenesis, cleavagewithin a range of nucleotides is generally sufficient, and cleavagebetween particular base pairs is not required.

As noted above, a fusion protein(s) can be expressed in a cell followingthe introduction, into the cell, of polypeptides and/or polynucleotides.For example, two polynucleotides, each comprising sequences encoding oneof the aforementioned polypeptides, can be introduced into a cell, andwhen the polypeptides are expressed and each binds to its targetsequence, cleavage occurs at or near the target sequence. Alternatively,a single polynucleotide comprising sequences encoding both fusionpolypeptides is introduced into a cell. Polynucleotides can be DNA, RNAor any modified forms or analogues or DNA and/or RNA.

In certain embodiments, targeted cleavage in a genomic region by a ZFNresults in alteration of the nucleotide sequence of the region,following repair of the cleavage event by non-homologous end joining(NHEJ).

In other embodiments, targeted cleavage in a genomic region by a ZFN canalso be part of a procedure in which a genomic sequence (e.g., a regionof interest in cellular chromatin) is replaced with a homologousnon-identical sequence (i.e., by targeted recombination) viahomology-dependent mechanisms (e.g., insertion of a donor sequencecomprising an exogenous sequence together with one or more sequencesthat are either identical, or homologous but non-identical, with apredetermined genomic sequence (i.e., a target site)). Becausedouble-stranded breaks in cellular DNA stimulate cellular repairmechanisms several thousand-fold in the vicinity of the cleavage site,targeted cleavage with ZFNs as described herein allows for thealteration or replacement (via homology-directed repair) of sequences atvirtually any site in the genome.

Targeted replacement of a selected genomic sequence requires, inaddition to the ZFNs described herein, the introduction of an exogenous(donor) polynucleotide. The donor polynucleotide can be introduced intothe cell prior to, concurrently with, or subsequent to, expression ofthe ZFNs. The donor polynucleotide contains sufficient homology to agenomic sequence to support homologous recombination (orhomology-directed repair) between it and the genomic sequence to whichit bears homology. Approximately 25, 50 100, 200, 500, 750, 1,000,1,500, 2,000 nucleotides or more of sequence homology (or any integralvalue between 10 and 2,000 nucleotides, or more) will support homologousrecombination. Donor polynucleotides can range in length from 10 to5,000 nucleotides (or any integral value of nucleotides therebetween) orlonger.

It will be readily apparent that the nucleotide sequence of the donorpolynucleotide is typically not identical to that of the genomicsequence that it replaces. For example, the sequence of the donorpolynucleotide can contain one or more substitutions, insertions,deletions, inversions or rearrangements with respect to the genomicsequence, so long as sufficient homology with chromosomal sequences ispresent. Such sequence changes can be of any size and can be as small asa single nucleotide pair. Alternatively, a donor polynucleotide cancontain a non-homologous sequence (i.e., an exogenous sequence, to bedistinguished from an exogenous polynucleotide) flanked by two regionsof homology. Additionally, donor polynucleotides can comprise a vectormolecule containing sequences that are not homologous to the region ofinterest in cellular chromatin. Generally, the homologous region(s) of adonor polynucleotide will have at least 50% sequence identity to agenomic sequence with which recombination is desired. In certainembodiments, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or 99.9% sequenceidentity is present. Any value between 1% and 100% sequence identity canbe present, depending upon the length of the donor polynucleotide.

A donor molecule can contain several, discontinuous regions of homologyto cellular chromatin. For example, for targeted insertion of sequencesnot normally present in a region of interest, said sequences can bepresent in a donor nucleic acid molecule and flanked by regions ofhomology to sequence in the region of interest.

To simplify assays (e.g., hybridization, PCR, restriction enzymedigestion) for determining successful insertion of sequences from thedonor polynucleotide, certain sequence differences may be present in thedonor sequence as compared to the genomic sequence. Preferably, iflocated in a coding region, such nucleotide sequence differences willnot change the amino acid sequence, or will make silent amino acidchanges (i.e., changes which do not affect the structure or function ofthe protein). The donor polynucleotide can optionally contain changes insequences corresponding to the zinc finger domain binding sites in theregion of interest, to prevent cleavage of donor sequences that havebeen introduced into cellular chromatin by homologous recombination.

A polynucleotide can be introduced into a cell as part of a vectormolecule having additional sequences such as, for example, replicationorigins, promoters and genes encoding antibiotic resistance. Moreover,donor polynucleotides can be introduced as naked nucleic acid, asnucleic acid complexed with an agent such as a liposome or poloxamer, orcan be delivered by bacteria or viruses (e.g., Agrobacterium, Rhizobiumsp. NGR234, Sinorhizoboium meliloti, Mesorhizobium loti, tobacco mosaicvirus, potato virus X, cauliflower mosaic virus and cassava vein mosaicvirus. See, e.g., Chung et al. (2006) Trends Plant Sci. 11(1):1-4.

For alteration of a chromosomal sequence, it is not necessary for theentire sequence of the donor to be copied into the chromosome, as longas enough of the donor sequence is copied to effect the desired sequencealteration.

The efficiency of insertion of donor sequences by homologousrecombination is inversely related to the distance, in the cellular DNA,between the double-stranded break and the site at which recombination isdesired. In other words, higher homologous recombination efficienciesare observed when the double-stranded break is closer to the site atwhich recombination is desired. In cases in which a precise site ofrecombination is not predetermined (e.g., the desired recombinationevent can occur over an interval of genomic sequence), the length andsequence of the donor nucleic acid, together with the site(s) ofcleavage, are selected to obtain the desired recombination event. Incases in which the desired event is designed to change the sequence of asingle nucleotide pair in a genomic sequence, cellular chromatin iscleaved within 10,000 nucleotides on either side of that nucleotidepair. In certain embodiments, cleavage occurs within 1,000, 500, 200,100, 90, 80, 70, 60, 50, 40, 30, 20, 10, 5, or 2 nucleotides, or anyintegral value between 2 and 1,000 nucleotides, on either side of thenucleotide pair whose sequence is to be changed.

Targeted insertion of exogenous sequences into a genomic region isaccomplished by targeted cleavage in the genomic region using ZFNs, inconcert with provision of an exogenous (donor) polynucleotide containingthe exogenous sequences. The donor polynucleotide also typicallycontains sequences flanking the exogenous sequence, which containssufficient homology to the genomic region to support homology-directedrepair of the double-strand break in the genomic sequence, therebyinserting the exogenous sequence into the genomic region. Therefore, thedonor nucleic acid can be of any size sufficient to support integrationof the exogenous sequence by homology-dependent repair mechanisms (e.g.,homologous recombination). Without wishing to be bound by any particulartheory, the regions of homology flanking the exogenous sequence arethought to provide the broken chromosome ends with a template forre-synthesis of the genetic information at the site of thedouble-stranded break.

Targeted integration of exogenous sequences, as described above, can beused to insert a marker gene at a chosen chromosomal location. Markergenes include, but are not limited to, sequences encoding proteins thatmediate antibiotic resistance (e.g., ampicillin resistance, neomycinresistance, G418 resistance, puromycin resistance), sequences encodingcolored or fluorescent or luminescent proteins (e.g., green fluorescentprotein, enhanced green fluorescent protein, red fluorescent protein,luciferase), and proteins which mediate enhanced cell growth and/or geneamplification (e.g., dihydrofolate reductase). Exemplary marker genesthus include, but are not limited to, β-glucuronidase (GUS),phosphinothricin N-acetyl transferase (PAT, BAR), neomycinphosphotransferase, β-lactamase, catechol dioxygenase, α-amylase,tyrosinase, β-galactosidase, luciferase, aequorin, EPSP synthase,nitrilase, acetolactate synthase (ALS), dihydrofolate reductase (DHFR),dalapon dehalogenase and anthranilate synthase. In certain embodiments,targeted integration is used to insert a RNA expression construct, e.g.,sequences responsible for regulated expression of micro RNA or siRNA.Promoters, enhancers and additional transcription regulatory sequencescan also be incorporated in a RNA expression construct.

Further increases in efficiency of targeted recombination, in cellscomprising a zinc finger/nuclease fusion molecule and a donor DNAmolecule, are achieved by blocking the cells in the G₂ phase of the cellcycle, when homology-driven repair processes are maximally active. Sucharrest can be achieved in a number of ways. For example, cells can betreated with e.g., drugs, compounds and/or small molecules whichinfluence cell-cycle progression so as to arrest cells in G₂ phase.Exemplary molecules of this type include, but are not limited to,compounds which affect microtubule polymerization (e.g., vinblastine,nocodazole, Taxol), compounds that interact with DNA (e.g.,cis-platinum(II) diamine dichloride, Cisplatin, doxorubicin) and/orcompounds that affect DNA synthesis (e.g., thymidine, hydroxyurea,L-mimosine, etoposide, 5-fluorouracil). Additional increases inrecombination efficiency are achieved by the use of histone deacetylase(HDAC) inhibitors (e.g., sodium butyrate, trichostatin A) which alterchromatin structure to make genomic DNA more accessible to the cellularrecombination machinery.

Additional methods for cell-cycle arrest include overexpression ofproteins which inhibit the activity of the CDK cell-cycle kinases, forexample, by introducing a cDNA encoding the protein into the cell or byintroducing into the cell an engineered ZFP which activates expressionof the gene encoding the protein. Cell-cycle arrest is also achieved byinhibiting the activity of cyclins and CDKs, for example, using RNAimethods (e.g., U.S. Pat. No. 6,506,559) or by introducing into the cellan engineered ZFP which represses expression of one or more genesinvolved in cell-cycle progression such as, for example, cyclin and/orCDK genes. See, e.g., co-owned U.S. Pat. No. 6,534,261 for methods forthe synthesis of engineered zinc finger proteins for regulation of geneexpression.

As described above, the disclosed methods and compositions for targetedcleavage can be used to induce mutations in a genomic sequence. Targetedcleavage can also be used to create gene knock-outs (e.g., forfunctional genomics or target validation) and to facilitate targetedinsertion of a sequence into a genome (i.e., gene knock-in). Insertioncan be by means of replacements of chromosomal sequences throughhomologous recombination or by targeted integration, in which a newsequence (i.e., a sequence not present in the region of interest),flanked by sequences homologous to the region of interest in thechromosome, is inserted at a predetermined target site. The same methodscan also be used to replace a wild-type sequence with a mutant sequence,or to convert one allele to a different allele.

Targeted cleavage of infecting or integrated plant pathogens can be usedto treat pathogenic infections in a plant host, for example, by cleavingthe genome of the pathogen such that its pathogenicity is reduced oreliminated. Additionally, targeted cleavage of genes encoding receptorsfor plant viruses can be used to block expression of such receptors,thereby preventing viral infection and/or viral spread in the plant.

Exemplary plant pathogens include, but are not limited to, plant virusessuch as Alfamoviruses, Alphacryptoviruses, Badnaviruses,Betacryptoviruses, Bigeminiviruses, Bromoviruses, Bymoviruses,Capilloviruses, Carlaviruses, Carmoviruses, Caulimoviruses,Closteroviruses, Comoviruses, Cucumoviruses, Cytorhabdoviruses,Dianthoviruses, Enamoviruses, Fabaviruses, Fijiviruses, Furoviruses,Hordeiviruses, Hybrigeminiviruses, Idaeoviruses, Ilarviruses,Ipomoviruses, Luteoviruses, Machlomoviruses, Macluraviruses,Marafiviruses, Monogeminiviruses, Nanaviruses, Necroviruses,Nepoviruses, Nucleorhabdoviruses, Oryzaviruses, Ourmiaviruses,Phytoreoviruses, Potexviruses, Potyviruses, Rymoviruses, satellite RNAs,satelliviruses, Sequiviruses, Sobemoviruses, Tenuiviruses,Tobamoviruses, Tobraviruses, Tombusviruses, Tospoviruses, Trichoviruses,Tymoviruses, Umbraviruses, Varicosaviruses and Waikaviruses; fungalpathogens such as smuts (e.g. Ustilaginales), rusts (Uredinales), ergots(Clavicepts pupurea) and mildew; molds (Oomycetes) such as Phytophthorainfestans (potato blight); bacterial pathogens such as Erwinia (e.g., E.herbicola), Pseudomonas (e.g., P. aeruginosa, P. syringae, P.fluorescense and P. putida), Ralstonia (e.g., R. solanacearum),Agrobacterium and Xanthomonas; roundworms (Nematoda); and Phytomyxea(Polymyxa and Plasmodiophora).

The disclosed methods for targeted recombination can be used to replaceany genomic sequence with a homologous, non-identical sequence. Forexample, a mutant genomic sequence can be replaced by its wild-typecounterpart, thereby providing methods for treatment of plant diseases;providing resistance to plant pathogens; increasing crop yields, etc. Inlike fashion, one allele of a gene can be replaced by a different alleleusing the methods of targeted recombination disclosed herein.

In many of these cases, a region of interest comprises a mutation, andthe donor polynucleotide comprises the corresponding wild-type sequence.Similarly, a wild-type genomic sequence can be replaced by a mutantsequence, if such is desirable. Indeed, any pathology dependent upon aparticular genomic sequence, in any fashion, can be corrected oralleviated using the methods and compositions disclosed herein.

Targeted cleavage and targeted recombination can also be used to alternon-coding sequences (e.g., regulatory sequences such as promoters,enhancers, initiators, terminators, splice sites) to alter the levels ofexpression of a gene product. Such methods can be used, for example, fortherapeutic purposes, alterations in cellular physiology andbiochemistry, functional genomics and/or target validation studies.

The methods and compositions described herein can also be used foractivation and repression of gene expression using fusions between anon-canonical zinc finger binding domain and a functional domain. Suchmethods are disclosed, for example, in co-owned U.S. Pat. Nos.6,534,261; 6,824,978 and 6,933,113; the disclosures of which areincorporated by reference. Additional repression methods include the useof antisense oligonucleotides and/or small interfering RNA (siRNA orRNAi) targeted to the sequence of the gene to be repressed.

In additional embodiments, one or more fusions between a zinc fingerbinding domain and a recombinase (or functional fragment thereof) can beused, in addition to or instead of the zinc finger-cleavage domainfusions disclosed herein, to facilitate targeted recombination. See, forexample, co-owned U.S. Pat. No. 6,534,261 and Akopian et al. (2003)Proc. Natl. Acad. Sci. USA 100:8688-8691.

In additional embodiments, the disclosed methods and compositions areused to provide fusions of ZFP binding domains with transcriptionalactivation or repression domains that require dimerization (eitherhomodimerization or heterodimerization) for their activity. In thesecases, a fusion polypeptide comprises a zinc finger binding domain and afunctional domain monomer (e.g., a monomer from a dimerictranscriptional activation or repression domain). Binding of two suchfusion polypeptides to properly situated target sites allowsdimerization so as to reconstitute a functional transcription activationor repression domain.

EXAMPLES

The present invention is further defined in the following Examples, inwhich all parts and percentages are by weight and degrees are Celsius,unless otherwise stated. It should be understood that these Examples,while indicating certain embodiments of the invention, are given by wayof illustration only. From the above discussion and these Examples, oneskilled in the art can ascertain the essential characteristics of thisinvention, and without departing from the spirit and scope thereof, canmake various changes and modifications of the invention to adapt it tovarious usages and conditions.

Example 1 ZFN Expression Vectors

Expression vectors comprising sequences encoding 4-fingered ZFNs(designated “5-8” and “5-9”) as described in Examples 2 and 14 of U.S.Patent Publication 2005/0064474, the disclosure of which is incorporatedby reference (See Example 2 of that application) were modified asfollows. Briefly, the 5-8 and 5-9 ZFN (comprising 4 zinc finger domainsfused to the nuclease domain of the type IIS restriction enzyme FokI(amino acids 384-579 of the sequence of Wah et al. (1998) Proc. Natl.Acad. Sci. USA 95:10564-10569) via a four amino acid ZC linker) weremodified to a CCHC structure. Additional modifications (substitutionsand insertions) were also made to residues between the C-terminal Hisand Cys zinc coordinating structures and/or C-terminal to the C-terminalCys to finger 2 and/or finger 4.

Example 2 Gene Correction of eGFP in Reporter Cell Lines

The ability of ZFNs comprising CCHC zinc fingers as described herein tofacilitate homologous recombination was tested in the GFP systemdescribed in Urnov (2005) Nature 435(7042):646-51 and U.S. PatentPublication No. 20050064474 (e.g., Examples 6-11). Briefly, 50 ng ofeach ZFN and 500 ng of the promoter-less GFP donor (Urnov (2005) Nature)were transfected into 500,000 reporter cells, using 2 uL ofLipofectamine 2000 per sample, as per the Invitrogen Lipofectamine 2000protocol.

Vinblastine was added 24 hours post-transfection at a 0.2 uM finalconcentration, and was removed 72 hours post-transfection.

The cells were assayed for GFP expression 5 days post-transfection bymeasuring 40,000 cells per transfection on the Guava bench top FACSanalyzer.

As shown in FIG. 1, most ZFNs comprising altered CCHC zinc fingers asshown in Tables 1 and 2 above facilitate homologous recombination at thereporter (GFP) locus, resulting in GFP expression at levels aboveunmodified CCHC zinc fingers and several performed comparably to ZFNscomprising CCHH zinc fingers. The optimal performing variant whenpositioned in finger 4 (F4) comprised the following sequence (includingand C-terminal to the His zinc coordinating residue): HAQRCGLRGSQLV (SEQID NO:53) (the zinc finger in Table 2 designated #21 and shown in FIG. 1as “2-21”). The optimal performing variant when positioned in finger 2(F2) comprised the following sequence (including and C-terminal to theHis zinc coordinating residue): HIRTCTGSQKP (SEQ ID NO:75) (the zincfinger in Table 2 designated #43 and shown in FIG. 1 as “2-43”).

Example 3 Editing of a Chromosomal IL2Rγ Gene by Targeted Recombination

ZFNs as described herein were also assayed in the endogenous IL2Rγ assaydescribed in Urnov (2005) Nature 435(7042):646-51 and Example 2 of U.S.Patent Publication No. 20050064474. Briefly, two and a half microgramseach ZFN expression construct were transfected into 500,000 K562 cellsusing a Nucleofector (Amaxa). Genomic DNA was harvested and genedisruption was assayed at the endogenous IL2Rγ locus using the Surveyorendonuclease kit.

ZFNs are shown in the upper left of FIG. 2. In particular, altered zincfinger 20 refers to a CCHC zinc finger comprising the sequenceHTRRCGLRGSQLV; zinc finger 21 comprises the sequence HAQRCGLRGSQLV (SEQID NO:53); zinc finger 43 comprises the sequence HIRTCTGSQKP (SEQ IDNO:75); zinc finger 45 comprises the sequence HIRTGCTGSQKP; zinc finger47 comprises the sequence HIRRCTGSQKP; and zinc finger 48 comprises thesequence HIRRGCTGSQKP. Zinc fingers 20 and 21 were used in finger 4 ofthe 4-fingered ZFNs and zinc fingers 43, 45, 47, and 48 were used infinger 2 of the 4-fingered ZFNs.

The pairs of ZFNs tested are shown in FIG. 2 above and to the right ofthe graph and in Table 5:

TABLE 5 Sample # 5-8 ZFN 5-9 ZFN 1 None (GFP) 2 wild type (CCHH) wildtype (CCHH) 3 43 (finger 2) 43 (finger 2) 4 43 (finger 2) 20 (finger 4)5 43 (finger 2) 21 (finger 4) 6 43 (finger 2) 45 (finger 2) 7 43 (finger2) 47 (finger 2) 8 20 (finger 4) 43 (finger 2) 9 21 (finger 4) 43(finger 2) 10 45 (finger 2) 43 (finger 2) 11 47 (finger 2) 43 (finger 2)12 48 (finger 2) 43 (finger 2)

To determine if mutations had been induced at the cleavage site, theamplification product was analyzed using a Cel-1 assay, in which theamplification product is denatured and renatured, followed by treatmentwith the mismatch-specific Cel-1 nuclease. See, for example, Oleykowskiet al. (1998) Nucleic Acids res. 26:4597-4602; Qui et al. (2004)BioTechniques 36:702-707; Yeung et al. (2005) BioTechniques 38:749-758.

Results of two experiments are shown for each sample in FIG. 2.Experiment #2 for samples 8 and 9 had significant background noise inthe lanes which reduced the apparent efficacy of these ZFNs.

As shown in FIG. 2, certain CCHC variants are essentially equivalent tothe wild-type C2H2 ZFNs. Zinc finger 21 at finger 4 (samples 5 and 9)produced better results than zinc finger 20 at finger 4 (samples 4 and8). In Finger 2, zinc finger 43 produced the best results.

Example 4 Gene Correction of eGFP in Reporter Cell Lines

Based on the results shown in FIGS. 1 and 2, CCHC zinc fingers shown inTables 3 and 4 above (designated 1a through 10a) were produced. Thesezinc fingers were incorporated into the 5-8 and 5-9 ZFNs and tested inthe GFP gene correction assay described in Example 2 above. The ZFNpairs tested in each sample are shown below each bar, where the zincfinger numbers 20, 21, 43, 45, 47 and 48 are those described in Example3 and CCHC zinc fingers 1a through 10a comprise the sequence shown inTables 3 and 4 above. Zinc fingers 20, 21, 7a, 8a, 9a and 10a were usedin Finger 4; zinc fingers 43, 45, 47, 48, 1a, 2a, 3a, 4a, 5a, and 6awere used in Finger 2.

Results are shown in FIG. 3. The top row beneath each bar refers to thezinc finger incorporated into ZFN 5-8 and the bottom row beneath eachbar refers to the zinc finger incorporated into ZFN 5-9. For example,the 2^(nd) bar from the left on the graph of FIG. 3 refers to a sampletransfected with 5-8 and 5-9 ZFNs in which F4 of both ZFNs comprises thesequence of zinc finger 20. As shown, many of the ZFNs comprising CCHCzinc fingers performed comparable to wild type (CCHH) ZFNs.

Example 5 Design and Generation of Target Vector A. Overall Structure ofthe Target Sequence

The target construct for tobacco (a dicot) included the following 7components as shown in FIGS. 4 and 5: i) a hygromycin phosphotransferase(HPT) expression cassette comprising an A. thaliana ubiguitin-3 (ubi-3)promoter (Callis, et al., 1990, J. Biol. Chem. 265-12486-12493) drivingthe E. coli HPT gene (Waldron et al., 1985, Plant Mol. Biol. 18:189-200)terminated by an A. tumifaciens open reading frame-24 (orf-24) 3′untranslated region (UTR) (Gelvin et al., 1987, EP222493); ii)homologous sequence-1, comprising the N. tabacum RB7 matrix attachmentregion (MAR) (Thompson et al., 1997, WO9727207); iii) a 5′ GreenFluorescent Protein (GFP) gene fragment (Evrogen Joint Stock Company,Moscow, Russia) driven by a modified A. tumifaciens mannopine synthase(Δmas) promoter (Petolino et al., U.S. Pat. No. 6,730,824); iv) aβ-glucuronidase (GUS) expression cassette comprising a Cassava VeinMosaic Virus (CsVMV) promoter (Verdaguer et al., 1996, Plant MolecularBiology 31:1129-1139) driving a GUS gene (Jefferson, 1987, Plant Mol.Biol. Rep. 5:387-405) terminated by the A. tumifaciens nopaline synthase(nos) 3′UTR (DePicker et al., 1982, J. Mol. Appl. Genet. 1:561-573); v)a 3′ GFP gene fragment (Evrogen Joint Stock Company, Moscow, Russia)terminated by an A. tumifaciens orf-1 3′ UTR (Huang et al., J.Bacteriol. 172:1814-1822); vi) homologous sequence-2, comprising A.thaliana 4-coumaroyl-CoA synthase (4-CoAS) intron-1 (Locus At3g21320,GenBank NC 003074) and; vii) a S. viridochromogenes phosphinothricinphosphotransferase (PAT) (Wohlleben et al., 1988, Gene 70:25-37) 3′ genefragment terminated byA. tumifaciens ORF-25/26 3′ UTR (Gelvin et al.,1987, EP222493).

A zinc finger-FokI fusion protein binding site (IL-1-L0-Fok1) (Urnov etal., 2005, US 2005/0064474) was inserted down stream of the CsVMVpromoter (Verdaguer et al., 1996, Plant Molecular Biology 31:1129-1139)and fused with the GUS coding sequence (Jefferson, 1987, Plant Mol.Biol. Rep. 5:387-405) at the N-terminal. Two copies of a second zincfinger-Fok1 fusion protein binding site (Scd27-L0-Fok1) (Urnov et al.,2005, US 2005/0064474) flanked the 5′ and 3′ GFP gene fragments (EvrogenJoint Stock Company, Moscow, Russia). Each binding site contained fourtandem repeats of the recognition sequence of the particular zincfinger-Fok1 fusion protein so that each binding site was 200 bp in size(FIG. 6A). This was designed to ensure that the recognition sequenceswould be accessible to the zinc finger-Fok1 fusion protein in thecomplex chromatin environment. Each recognition sequence included aninverted repeat sequence to which a single zinc finger-Fok1 fusionprotein bound as a homodimer and cleaved the double stranded DNA (FIG.6B). The 5′ and 3′ GFP gene fragments overlapped by 540 bp providinghomology within the target sequence and a stop codon was inserted at the3′ end of the 5′ GFP fragment to ensure no functional GFP translationfrom the target sequence.

The transformation vector comprising the target sequence was generatedthrough a multiple-step cloning process as described below.

B. Construction of the HPT Binary Vector (pDAB1584)

The vector pDAB1400, which contained a GUS expression cassette,comprising an A. thaliana ubi-3 promoter (Callis, et al., 1990, J. Biol.Chem. 265-12486-12493) driving the GUS gene (Jefferson, 1987, Plant Mol.Biol. Rep. 5:387-405) terminated by A. tumifaciens orf-1 UTR (Huang etal., J. Bacteriol. 172:1814-1822), was used as the starting baseconstruct (FIG. 7).

To avoid any unnecessary repeated regulatory elements in the targetconstruct, the A. tumifaciens orf-1 UTR (Huang et al., J. Bacteriol.172:1814-1822) in pDAB1400 was replaced with an A. tumifaciens orf-24UTR (Gelvin et al., 1987, EP222493), which was excised from pDAB782(FIG. 8) as a SacI/XbaI fragment and cloned into the same sites inpDAB1400. The resulting construct contained an A. thaliana ubi-3promoter (Callis, et al., 1990, J. Biol. Chem. 265-12486-12493) drivingthe GUS gene (Jefferson, 1987, Plant Mol. Biol. Rep. 5:387-405)terminated by an A. tumifaciens orf-24 UTR (Gelvin et al., 1987,EP222493) and was named pDAB1582 (FIG. 9).

The HPT coding sequence (Waldron et al., 1985, Plant Mol. Biol.18:189-200) was PCR amplified from pDAB354 plasmid (FIG. 10) using theprimers P1 and P2. A BbsI site was added at the 5′ end of primer P1 andthe SacI site was retained at the 3′ end of primer P2. The HPTII PCRfragment was digested with BbsI/SacI and cloned into pDAB1582 digestedwith NcoI-SacI to replace the GUS gene with the HPT gene from the PCRfragment. The resulting plasmid was named pDAB1583 (FIG. 11).

The A. thaliana ubi-3/HPT/A. tumifaciens orf-24 fragment was thenexcised from pDAB1583 by NotI digestion and treated with T4 DNApolymerase to generate blunt-ends. The blunt-end-treated HPT expressioncassette was cloned into pDAB2407 (FIG. 12), a binary base vector, atthe PmeI site resulting in plasmid pDAB1584 (FIG. 13).

C. Construction of the Vector Comprising the Homologous Sequences andthe Scd27 Zinc Finger-Fok1 Fusion Protein Binding Site (pDAB1580)

The A. tumefaciens orf-1 UTR (Huang et al., J. Bacteriol. 172:1814-1822)in pDAB2418 (FIG. 14) was replaced with the A. tumefaciens orf25/26 UTR(Gelvin et al., 1987, EP222493) to avoid repeated regulatory sequencesin the target vector. To make the UTR swap, the A. tumefaciens orf25/26UTR (Gelvin et al., 1987, EP222493) was PCR amplified from the pDAB4045plasmid (FIG. 15) using primers P3 and P4. Smal and Agel sites wereadded to the 3′ end of PCR fragment, and the SacI site was retained atthe 5′ end. The pDAB2418 plasmid DNA, which contained a PAT geneexpression cassette comprising the A. thaliana ubiquitin-10 (ubi-10)promoter (Callis, et al., 1990, J. Biol. Chem. 265-12486-12493) drivingthe PAT gene (Wohlleben et al., 1988, Gene 70:25-37) terminated by theA. tumefaciens orf-1 UTR (Huang et al., J. Bacteriol. 172:1814-1822) anda N. tabacum RB7 MAR sequence (Thompson et al., 1997, WO9727207), wasdigested with SacI and Agel and the two largest fragments wererecovered. These fragments were ligated with the A. tumefaciens orf25/26UTR (Gelvin et al., 1987, EP222493) PCR product digested with SacI andAgel. The resulting plasmid was named pDAB1575 (FIG. 16). The N. tabacumRB7 MAR (Thompson et al., 1997, WO9727207) serves as homologoussequence-1 in the target vector.

Intron-1 of A. thaliana 4-CoAS (Locus At3g21320, GenBank NC 003074) wasselected to serve as homologous sequence-2 in the target vector. The PATgene (Wohlleben et al., 1988, Gene 70:25-37) coding sequence wasanalyzed and the 299/300 bp downstream of the start codon was identifiedas the site for inserting the intron so that the appropriate 5′ and 3′splicing sites would be formed. The full-length intron was then fusedwith 253 bp of 3′ partial PAT coding sequence by DNA synthesis(Picoscript Ltd., LLP, Houston, Tex.). NotI and SacI sites were added tothe 5′ and 3′ end of the DNA fragment, respectively. The synthesized DNAfragment was then digested with NotI/SacI and inserted into pDAB1575 atthe same sites to replace the full-length PAT coding sequence. Theresulting construct was named pDAB1577 (FIG. 17).

A 241 bp DNA fragment containing 4 tandem repeats of Scd27-L0-Fok1recognition sites (FIG. 6) was synthesized (Picoscript Ltd., LLP,Houston, Tex.) with a Smal site added to both 5′ and 3′ ends of thefragment. The synthesized zinc finger-Fok1 binding site-containingfragment was then digested with Smal and inserted into pDAB1577 at MscIsite. The resulting vector was named pDAB1579 (FIG. 18). A secondSmaI-digested zinc finger-Fok1 binding site-containing fragment was theninserted into pDAB1579 at the SwaI site. The resulting construct wasnamed pDAB1580 (FIG. 19). This vector contains homologous sequences 1and 2 (N. tabacum RB7 MAR and A. thaliana 4-CoAS intron1, respectively)and two synthesized Scd27 zinc finger-Fok1 binding sites, eachcontaining 4 tandem repeats of Scd27-L0-Fok1 recognition sites.

D. Construction of the Vector Containing Two Partially DuplicatedNon-Functional GFP Fragments (pDAB1572)

The GFP gene, CopGFP, was purchased from Evrogen Joint Stock Company(Moscow, Russia) and the full-length coding sequence was PCR amplifiedusing primers P5 and P6. BbsI and SacI sites were added to the 5′ and 3′ends of the PCR product, respectively. The CopGFP PCR product was thendigested with BbsI/SacI and cloned into pDAB3401 (FIG. 20) comprisingthe modified A. tumifaciens Δmas promoter (Petolino et al., U.S. Pat.No. 6,730,824) driving the GUS gene (Jefferson, 1987, Plant Mol. Biol.Rep. 5:387-405) and terminated by A. tumifaciens orf-1 3′ UTR (Huang etal., J. Bacteriol. 172:1814-1822) at the NcoI/SacI sites to replace theGUS gene. The resulting vector was named pDAB1570 (FIG. 21).

To make the two partially duplicated, non-functional GFP fragments, aDNA fragment containing the majority of the coding sequence of CopGFPwith a 47 bp deletion at the 5′ end was PCR amplified using primers P9and P10. An ApaI site was added to both the 5′ and 3′ ends and anadditional StuI site was added to the 5′ end downstream of the ApaIsite. The PCR product was then digested with ApaI and inserted intopDAB1570 at the ApaI site, thereby creating two non-functional GFPfragments in the same vector with a 540 bp duplicated sequence. Theresultant construct was named pDAB1572 (FIG. 22).

E. Construction of the Vector Containing the IL-1 Zinc Finger-Fok1Fusion Protein Binding Site/GUS Gene Fusion (pDAB1573)

A 233 bp DNA fragment containing 4 tandem repeats of IL-1_L0-Fok1recognition site (FIG. 6) was synthesized by Picoscript Ltd., LLP,(Houston, Tex.) with NcoI and AflIII sites added to the 5′ and 3′ ends,respectively. The synthesized fragment was then digested withNcoI/AflIII and inserted into pDAB4003 (FIG. 23), which contained a GUSgene (Jefferson, 1987, Plant Mol. Biol. Rep. 5:387-405) driven by aCsVMV promoter (Verdaguer et al., 1996, Plant Molecular Biology31:1129-1139) terminated by A. tumefaciens orf-1 3′ UTR (Huang et al.,J. Bacteriol. 172:1814-1822) at NcoI site. An N-terminal fusion betweenIL-1_Lo-Fok1 binding site and GUS coding sequence was then generated.The resulting vector was named pDAB1571 (FIG. 24).

To avoid repeat 3′ UTR elements in the target vector, the A. tumefaciensnos 3′ UTR (DePicker et al., 1982, J. Mol. Appl. Genet. 1:561-573) wasexcised from pDAB7204 (FIG. 25) as a SacI/PmeI fragment and cloned intopDAB1571, which was digested with SacI/NaeI, to replace the A.tumefaciens orf-1 3′ UTR (Huang et al., J. Bacteriol. 172:1814-1822).The resulting plasmid was named pDAB1573 (FIG. 26).

F. Construction of the Final Target Vector (pDAB1585)

To make to final target vector, the GUS expression cassette with theIL-1-Fok1 fusion protein target site insertion was excised from pDAB1573by NotI digestion, blunt-end treated and inserted into pDAB1572 at StuIsite. The resulting intermediate vector was named pDAB1574 (FIG. 27).The entire cassette containing the modified Δmas promoter (Petolino etal., U.S. Pat. No. 6,730,824), a 5′ partially duplicated GFP sequence(Evrogen Joint Stock Company, Moscow, Russia), the CsVMV promoter(Verdaguer et al., 1996, Plant Molecular Biology 31:1129-1139), anIL-1-Fok1 fusion protein target sequence, the GUS gene (Jefferson, 1987,Plant Mol. Biol. Rep. 5:387-405) coding region, an A. tumefaciens nos 3′UTR (DePicker et al., 1982, J. Mol. Appl. Genet. 1:561-573), a 3′partially duplicated GFP (Evrogen Joint Stock Company, Moscow, Russia)and A. tumefaciens orf-1 3′ UTR (Huang et al., J. Bacteriol.172:1814-1822) was excised from pDAB1574 and inserted into pDAB1580 atthe NotI site. The resulting plasmid was named pDAB1581 (FIG. 28). TheAgel fragment of pDAB1581 was then inserted into pDAB1584 at Agel sitethereby creating the final target construct, pDAB1585 (FIGS. 4 and 5).

Example 6 Generation of Transgenic Cell Lines with Integrated TargetSequences

A tobacco cell suspension culture, referred to as BY2, was used intowhich target sequences of Example 5 were stably integrated viaAgrobacterium transformation. The base cell line, BY2, was obtained fromJun Ueki of Japan Tobacco, Iwata, Shizuoka, Japan. This cultureproliferates as 5-10 μ diameter cells in 100-150 cell clusters with adoubling time of roughly 18 hours. BY2 cell suspension cultures weremaintained in media containing LS basal salts (PhytoTechnology LabsL689), 170 mg/L KH₂PO₄, 30 g/L sucrose, 0.2 mg/L 2,4-D and 0.6 mg/Lthiamine-HCL at a pH of 6.0. The BY2 cells were sub-cultured every 7days by adding 50 mL of LS-based medium to 0.25 mL PCV. The BY2 cellsuspension culture was maintained in 250-mL flasks on a rotary shaker at25° C. and 125 RPM.

In order to generate transgenic BY2 cell culture with integrated targetsequences, a flask of a four-day post sub-culture tobacco suspension wasdivided into 10-12 four mL aliquots which were co-cultivated in 100×25mm Petri dishes with 100 μL Agrobacterium strain LBA4404 harboringpDAB1585 grown overnight to an OD₆₀₀˜1.5. Dishes were wrapped withparafilm and incubated at 25° C. without shaking for 3 days after whichexcess liquid was removed and replaced with 11 mL of LS-based basalmedium containing 500 mg/L carbenicillin.

Following re-suspension of the tobacco cells, 1 mL suspension wasdispensed onto 100×25 mm plates of appropriate base medium containing500 mg/L carbenicillin and 200 mg/L hygromycin solidified with 8 g/L TCagar, and incubated unwrapped at 28° C. in the dark. This resulted in122-144 selection plates for a single treatment. Individualhygromycin-resistant isolates appeared 10-14 days after plating and weretransferred to individual 60×20 mm plates (one isolate per plate) wherethey were maintained as callus on a 14-day subculture schedule untilneeded for analysis and subsequent re-transformation experiments.

Example 7 Screening and Characterization of Target Transgenic Events

The hygromycin-resistant transgenic events generated from thetransformation of target vector into BY2 tobacco cell cultures, asdescribed in Example 6 were analyzed as follows.

The initial analyses conducted for screening these transgenic eventsincluded GUS expression analysis to indicate the accessibility of thetarget sequence, PCR analysis of the partial and full-length targetsequence to confirm the presence and intactness of target vector andSouthern blot analysis to determine the copy number of the integratedtarget sequence. A subset of the transgenic events that showed GUSexpression contained one single copy of full length target sequence;these were selected for re-establishing suspension cultures to generatethe target lines for subsequent re-transformation. These re-establishedtarget lines were also subjected further characterization, whichincluded more thorough Southern blot analysis, sequencing confirmationof the entire target insert and flanking genomic sequence analysis.

Transgenic tobacco callus tissue or suspension cultures initiated fromthe selected events were analyzed for GUS activity by incubating 50 mgsamples in 150 μL of assay buffer for 24-48 hours at 37° C. The assaybuffer consisted of 0.2 M sodium phosphate pH 8.0, 0.1 mM each ofpotassium ferricyanide and potassium ferrocyanide, 1.0 mM sodium EDTA,0.5 mg/mL 5-bromo-4-chloro-3-indoyl-β-glucuronide and 0.6% (v/v) TritonX-100 (Jefferson, 1987, Plant Mol. Biol. Rep. 5:387-405). The appearanceof blue colored regions was used as the indicator of GUS geneexpression, which indicated that the target sequence insertion wastranscriptionally active and thus accessible in the local genomicenvironment.

The GUS expressing transgenic events were assayed by PCR using theprimer pair P15/P16 which led to amplification of a 10 kb DNA fragmentextending from the 3′ UTR of the HTP expression cassette at the 5′ endof target sequence to the 3′ UTR of the partial PAT gene cassette at the3′ end of the target sequence. Since all of the events were obtainedunder hygromycin selection, it was assumed that the HPT expressioncassette was intact in all of the target events. Therefore, only the 3′UTR of the HPT expression cassette was covered in the full length PCRanalysis. A subset of events were also PCR assayed using the primerpairs P15/P17 and P18/P19 to determine the intactness of the 5′ and 3′ends of the target sequence, respectively. All target events confirmedwith PCR analysis were further assayed by Southern blot analysis todetermine the copy number of the integrated target sequence.

Southern blot analysis was carried out for all target events that passedthe screening of GUS expression and full-length PCR. Ten fig of genomicDNA was digested with NsiI, which was a unique cutter within the targetsequence. The digested genomic DNA was separated on a 0.8% agarose geland transferred onto a nylon membrane. After cross-linking, thetransferred DNA on the membrane was hybridized with an HPT gene probe todetermine the copy number of the 5′ end of target sequence. The sameblot was then stripped and re-hybridized with a PAT gene probe todetermine the copy number of the 3′ end of the target sequence.

Multiple events that showed GUS expression and contained a single copyof full-length target sequence were selected for furthercharacterization, which included more thorough Southern blot analysis,entire target sequence confirmation and flanking genomic sequenceanalysis. One event, referred to as BY2-380, was selected based on themolecular characterization. Suspension culture was re-established fromthis event for subsequent re-transformation with vectors comprisingdonor DNA and non-C2H2 zinc finger-Fok1 fusion protein genes.

To ensure the suspension culture established from the target eventBY2-380 contained the intact target sequence as expected, the majortarget sequence from the 3′UTR of the HPT expression cassette at the 5′end of the target sequence to the 3′ UTR of the partial PAT genecassette at the 3′ end of the target sequence was PCR amplified usingthe primer pair P15/P16 and cloned into pCR2.1 TOPO vector (Invitrogen,Carlsbad, Calif.). The PCR products inserted in the TOPO vector weresequenced by Lark technology, Inc. (Houston, Tex.). The sequence resultsindicated that the BY2-380 had complete target sequences as expected.

The BY2-380 cell line was further analyzed to obtain the flankinggenomic sequences using the Universal GenomeWalker Kit (Clontech,Mountain View, Calif.). Brief, 2.5 μg of genomic DNA was digested withthree blunt-end restriction enzymes, EcoRV, DraI and StuI in separatereactions. The digested DNA was purified through phenol/chloroformextraction and ligated with BD GenomeWalker Adaptor. Nested PCRamplification was performed with the ligation as template and primer P20(walking upstream of the 5′ end of target sequence insertion) and P21(walking downstream of the 3′ end of target sequence insertion) for theprimary PCR reaction, and primer P22 (walking upstream of the 5′ end oftarget sequence insertion) and P23 (walking downstream of the 3′ end oftarget sequence insertion) for the secondary nested PCR reaction. Theamplified fragments from the secondary PCR reactions were cloned intopCR2.1 TOPO or pCR Blunt II TOPO vector (Invitrogen, Carlsbad, Calif.)and sequenced using a Dye Terminator Cycle Sequencing Kit (BeckmanCoulter, Fullerton, Calif.). The flanking genomic sequences wereobtained from the BY2-380 target line through this process. Primers werethen designed based on the flanking genomic sequences and used toamplify the entire target sequence.

The amplified fragments obtained from this target line was of expectedsize. Both ends of the amplified fragments were confirmed by sequencing.

Example 8 Design and Generation of Donor DNA Vector

The donor DNA construct included homologous sequence-1 (N. tabacum RB7MAR) (Thompson et al., 1997, WO9727207), a full-length A. thaliana ubi10promoter (Callis, et al., 1990, J. Biol. Chem. 265-12486-12493), 299 bpof 5′ partial PAT gene coding sequence (Wohlleben et al., 1988, Gene70:25-37) and homologous sequence-2 (A. thaliana 4-CoAS intron-1) (LocusAt3g21320, GenBank NC 003074). Both homologous sequence-1 and sequence-2in the donor vector were identical to the corresponding homologoussequence-1 and sequence-2 in the target vector (pDAB1585).

To construct the donor vector, the 299 bp of 5′ partial PAT codingsequence was fused with the full-length A. thaliana 4-CoAS intron-1(Locus At3g21320, GenBank NC 003074) through DNA synthesis by PicoscriptLtd., LLP, (Houston, Tex.). NcoI and XhoI sites were added to the 5′ and3′ end of the fragment, respectively. This synthesized DNA fragment wasthen digested with NcoI/XhoI and inserted into pDAB1575 at the samesites to replace the full-length PAT gene coding sequence and its 3′UTR. The resulting construct was named pDAB1576 (FIG. 29).

pDAB1576 was then digested with AgeI and the entire fragment containingthe 5′ partial PAT expression cassette flanked by homologous sequence-1and homologous sequence-2 was inserted into pDAB2407, the binary basevector, at the same site. The resultant construct was named pDAB1600(FIG. 30) and was the binary version of the donor vector for plant cellre-transformation.

Example 9 Design and Generation of Zinc Finger Nuclease ExpressionVectors

The zinc finger-Fok1 fusion protein gene was driven by a CsVMV promoterand 5′ UTR (Verdaguer et al., 1996, Plant Molecular Biology31:1129-1139). Also included in the cassette were an A. tumifaciens openreading frame-24 (orf-24) 3′ untranslated region (UTR) (Gelvin et al.,1987, EP222493).

To make these vectors, the C2H2 controls and their C3H variants ofIL-1-Fok1 and Scd27-Fok1 coding sequences described in Examples 1 to 4above were PCR amplified from their original designs with BbsI or NcoIand SacI sites added to the 5′ and 3′ end of the PCR fragments,respectively and cloned into the pDAB3731 (FIG. 31) digested withNcoI-SacI. The resultant plasmids were named pDAB4322 (FIG. 32),pDAB4331 (FIG. 33), pDAB4332 (FIG. 34), pDAB4333 (FIG. 35) pDAB4334(FIG. 36), pDAB4336 (FIG. 37), and pDAB4339 (FIG. 38). All of thesevectors contained the attL1 and attL2 sites flanking the ZFN expressioncassette and were compatible with Gateway™ cloning system (Invitrogen,Carlsbad, Calif.).

Two sets of binary version vectors were constructed for the IL-1-Fok1fusion protein. One contained the PAT selectable marker gene and theother did not contain the PAT selectable marker gene. For SCd27-Fok1fusion protein, only the binary version of vector without the PATselectable marker gene was constructed. To make the binary vectors withPAT selectable marker gene, the IL-1-FokI fusion protein expressioncassette in pDAB4322, pDAB4331, pDAB4332, pDAB4333, pDAB4334, andpDAB4336 were cloned into pDAB4321 (FIG. 39) through LR recombinationreaction using the LR Clonase™ Enzyme Mix (Invitrogen, Carlsbad,Calif.). The resultant plasmid were named pDAB4323 (FIG. 40), pDAB4341(FIG. 41), pDAB4342 (FIG. 42), pDAB4343 (FIG. 43), pDAB4344 (FIG. 44),pDAB4346 (FIG. 45). To make the binary vectors without the PATselectable marker gene, the C2H2 IL-1-FokI, C3H IL-1-FokI and Scd27-FokIexpression cassette in the pDAB4331, pDAB4336 and pDAB4339,respectively, were cloned into pDAB4330 (FIG. 46) through LRrecombination reaction using the LR Clonase™ Enzyme Mix (Invitrogen,Carlsbad, Calif.). The resultant plasmid were named pDAB4351 (FIG. 47),pDAB4356 (FIG. 48) and pDAB4359 (FIG. 49), respectively.

To make the C2H2 control of SCD27-FokI, the HindIII/SacI fragmentcomprising CsVMV promoter and 5′UTR driving PAT in pDAB7002 (FIG. 50)was replaced with a fragment comprising CsVMV promoter and 5′ UTR and N.tabacum 5′ UTR driving GUS, which was excised from pDAB7025 (FIG. 51)with HindIII/SacI. The resultant plasmid was named as pDAB1591 (FIG.52). The Scd27-L0-Fok1 coding sequences were PCR amplified from theiroriginal vectors pCDNA3.1-SCD27a-L0-FokI (FIG. 53) using primer pairP13/P14. BbsI and SacI sites were added to the 5′ and 3′ end of the PCRfragments, respectively. The PAT gene in pDAB1591 was replaced with thezinc finger fusion protein gene PCR fragment through SacI/NcoI cloning.The resultant plasmid was named pDAB1594 (FIG. 54). The binary versionof this vector was constructed by excising the zinc finger fusionprotein gene expression cassette from pDAB1594 as a PmeI/XhoI fragments,filling in the ends and cloning into pDAB2407 at the PmeI site. Theresultant plasmid was named pDAB1598 (FIG. 55). The details of allbinary vectors used for plant transformation is summarized in Table 6.

TABLE 6 Zinc Finger Nuclease Expression Vectors Finger Position of Typeof Zinc Amino Acid SEQ ID Vector ZFN ZFP finger Sequence NO: pDAB4323 IL1-FokI C2H2 F4 C . . . C . . . HTKIH 94 pDAB4341 IL 1-FokI. C2H2 F4 C .. . C . . . HTKIH 95 pDAB4342 IL 1- C3H F4 C . . . C . . . HTKIC 96FokI* pDAB4343 IL 1- C3H F4 C . . . C . . . HTKRCGGG 97 FokI* pDAB4344IL 1- C3H F4 C . . . C . . . HAQRCG 98 FokI* pDAB4346 IL 1- C3H F2 C . .. C . . . HIRTGC 99 FokI* pDAB4351 IL 1- C2H2 F4 C . . . C . . . HTKIH100 FokI* pDAB4356 IL 1- C3H F2 C . . . C . . . HIRTGC 101 FokI*pDAB1598 Scd27- C2H2 F4 C . . . C . . . HTKIH 102 FokI pDAB4359 Scd27-C3H F4 C . . . C . . . HAQRCGG 103 FokI* *FokI domain was plant codonbiased.

Example 10 Design and Generation of Positive Control Vector

To estimate the illegitimate recombination frequency and serve as apositive control, a vector containing the PAT gene expression cassettewas used. In order to be comparable with the final recombinants, the A.thaliana 4-CoAS intron-1 (Locus At3g21320, GenBank NC 003074) wasinserted at the 299/300 bp of the PAT coding sequence (Wohlleben et al.,1988, Gene 70:25-37). To make this construct, the 2559 bp SwaI/ClaIfragment from pDAB1576 was ligated with the backbone fragment ofpDAB1577 (FIG. 56) which was digested with the same restriction enzymes.The resulting vector contained the PAT gene expression cassette with the1743 bp of A. thaliana 4-CoAS intron-1 (Locus At3g21320, GenBank NC003074) (Locus At3g21320, GenBank NC 003074) insertion in the middle ofPAT coding sequence (Wohlleben et al., 1988, Gene 70:25-37). This vectorwas named pDAB1578 (FIG. 57).

To make the binary version of pDAB1578, the PAT gene expression cassettewith the A. thaliana intron-1 (Locus At3g21320, GenBank NC 003074) wasexcised from pDAB1578 with PmeI/XhoI. After the 3′ end of the fragmentwas blunt-end treated, it was inserted into pDAB2407, the binary basevector, at the PmeI site. The resulting vector was named pDAB1601 (FIG.58) which comprised the PAT gene (Wohlleben et al., 1988, Gene 70:25-37)containing A. thaliana 4-CoAS intron-1 (Locus At3g21320, GenBank NC003074) sequence driven by the A. thaliana ubi10 promoter (Callis, etal., 1990, J. Biol. Chem. 265-12486-12493) and terminated by the A.tumefaciens orf25/26 3′ UTR (Gelvin et al., 1987, EP222493).

Example 11 Demonstration of Intra-Chromosomal Homologous Recombinationby Re-transformation of Target Cell Cultures with C3H Zinc FingerNuclease Genes

To validate the functionality of C3H zinc finger nucleases instimulating intra-chromosomal homologous recombination, twononfunctional GFP fragments with 540 bp overlap sequences were includedin the target vector as shown in FIG. 59. In between these two fragmentswas a GUS gene expression cassette. The IL-1-Fok1 fusion protein bindingsequence was fused with the GUS coding sequence at its N-terminal.Without being bound by one theory, it was hypothesized that in thepresence of IL-1-Fok1 fusion protein, the IL-1 ZFN binding sequenceswould be recognized and a double stranded DNA break would be induced,which would stimulate the endogenous DNA repair process. Without thepresence of donor DNA, the two partially homologous GFP fragments wouldundergo an intra-chromosomal homologous recombination process and afunctional GFP gene would be reconstituted.

The BY2-380 transgenic cell line which contains a single, full-lengthintegrated copy of the target sequence was used to re-initiatesuspension cultures by placing˜250-500 mg of callus tissue into 40-50 mLof LS-based basal medium containing 100 mg/L hygromycin andsub-culturing every 7 days as described above. Prior tore-transformation, the suspension cultures were transferred to basalmedium without hygromycin for two passages, at least.

Agrobacterium-mediated transformation of the target cell cultures wasperformed as described above. For each experiment, 8 co-cultivationplates were generated as follows: one plate comprised cellsco-cultivated with 300 μL of base Agrobacterium strain LBA4404; oneplate comprised cells co-cultivated with 300 μL of an Agrobacteriumstrain harboring pDAB1590 (functional GFP construct); six plates eachcomprised cells co-cultivated with 300 μL of an Agrobacterium strainharboring pDAB4323, pDAB4341, pDAB4342, pDAB4343, pDAB4344, andpDAB4346, respectively. Following co-cultivation using the methodsdescribed above, the cells were plated out on eight plates containingthe LS-based basal medium supplemented with 500 mg/L carbenicillinwithout selection reagent. Apparent expression of the constitutedfunctional GFP gene resulted in visible fluorescence around 5-8 daysafter transformation). The number of green fluorescent loci per fieldwas counted by viewing 5 ‘random’ microscope fields per plate, 8 platesper constructs in each experiment, and averaged from 6 independentexperiments.

As summarized in Table 7, an average of 9.50 and 7.57 green fluorescentloci per field were observed from two C3H zinc finger nucleases,pDAB4346 and pDAB4343, respectively. These two C3H designs of IL-1-FokIperformed better than their C2H2 controls, pDAB4341 (6.37 loci perfield) and pDAB4323 (5.53 loci per field). Meanwhile, in comparison withthe C2H2 controls, the function of other two C3H variants of IL-1-FokIfusion protein, pDAB4344 (4.39 loci per field) and pDAB4342 (0.25 lociper field) was significantly impaired, in particular the pDAB4342, inwhich the C3H conversion was made simply by replacing the secondcysteine with histidine in the fourth finger. No appreciablefluorescence beyond slight background was observed in the negativecontrols transformed with the base Agrobacterium strain, LBA4404.

TABLE 7 Constitution of functional GFP through IL-1-Fok1 zinc fingerfusion protein-stimulated intra-chromosomal homologous recombinationVector Type of ZFP GFP expression Tukey Test** pDAB4346 C3H 9.50 ApDAB4343 C3H 7.57 B pDAB4341 C2H2 6.37 C pDAB4323* C2H2 5.53 D pDAB4344C3H 4.39 E pDAB4342 C3H 0.25 F *contains non-plant codon biased FokIdomain **Means not connected by the same letter are significantlydifferent at the 0.05 level

Example 12 Demonstration of Inter-Chromosomal Homologous Recombinationby Re-transformation of Target Cell Cultures with C3H Zinc FingerNuclease Genes and Donor DNA Sequences

To validate the functionality of C3H zinc finger-Fok1 fusion protein insimulating inter-chromosomal homologous recombination in the exemplarytobacco system, two strategies were developed and tested.

In strategy 1, the binding site for the zinc finger-Fok1 fusion protein(IL-1-L0-Fok1), was included in the middle of the target construct (FIG.61). In this strategy, the binding site was flanked by ˜3 kb ofnon-homologous sequences on both sides followed by homologous sequence-1(N. tabacum RB7 MAR) and homologous sequence-2 (A. thaliana 4-CoASintron-1) upstream and downstream, respectively. As demonstratedpreviously (e.g., U.S. Patent Publication No. 20050064474) in thepresence of C2H2 IL-1 zinc finger-Fok1 fusion protein, the IL-1-L0-Fok1binding sequences was recognized and a double stranded DNA break wasinduced at this specific site, which stimulated the endogenous DNArepair process. In the presence of donor DNA, which contained homologoussequences identical to that in the target sequence, the 5′ partial PATgene along with its promoter, replaced the entire ˜6 kb DNA fragmentbetween the homologous sequences in the target through homologousrecombination. Through this process, the two partial PAT gene sequences,with the A. thaliana 4-CoAS intron-1 interposed between, reconstituted afunctional PAT gene, resulting in PAT expression and an herbicideresistance phenotype.

In strategy 2, two zinc finger-Fok1 binding sites (Scd27-L0-Fok1) wereincluded in the target vector: one directly downstream of the N. tabacumRB7 MAR and the other directly upstream of the A. thaliana 4-CoASintron1 (FIG. 62). In between the two zinc finger-Fok1 fusion proteinbinding sites were ˜6 kb of sequence, which included the 5′ GFPfragment, a GUS expression cassette and the 3′ GFP fragment. Asdemonstrated previously (e.g., U.S. Patent Publication No. 20050064474),in the presence of Scd27 zinc finger-Fok1 fusion protein, the twobinding sequences recognized and double stranded DNA breaks were inducedat both locations, which removed the ˜6kb DNA fragment in between thesetwo binding sequences, and stimulated the endogenous DNA repair process.Similar to the strategy 1, in the presence of donor DNA, which containedhomologous sequences identical to that in the target sequence, the 5′partial PAT gene along with its promoter, was inserted into the targetsequence through homologous recombination at the site where the doublestrand DNA breaks were induced. Through this process, the two partialPAT gene sequences, with the A. thaliana 4-CoAS intron-1 interposedbetween, reconstituted a functional PAT gene, resulting in PATexpression and an herbicide resistance phenotype.

Agrobacterium-mediated transformation of the BY2-380 target cell culturewas performed as described above. For each experiment, 12 co-cultivationplates were generated as follows: one plate comprised cellsco-cultivated with 50 μL of an Agrobacterium strain harboring pDAB1600(donor DNA) and 250 μL Agrobacterium base strain, LBA4404; one platecomprised cells co-cultivated with 50 μL of an Agrobacterium strainharboring pDAB1601 (PAT selectable marker) and 250 μL Agrobacterium basestrain, LBA4404; two plates comprised cells co-cultivated with 50 μL ofan Agrobacterium strain harboring pDAB1600 (donor DNA) and 250 μL of anAgrobacterium strain harboring pDAB4351 (C2H2 IL-1 ZFP-Fok1); threeplates comprised cells co-cultivated with 50 μL of an Agrobacteriumstrain harboring pDAB1600 (donor DNA) and 250 μL of an Agrobacteriumstrain harboring pDAB4356 (C3H IL-1 ZFP-Fok1); two plates comprisedcells co-cultivated with 50 μL of an Agrobacterium strain harboringpDAB1600 (donor DNA) and 250 μL of an Agrobacterium strain harboringpDAB1598 (C2H2 Scd 27a ZFP-Fok1); three plates comprised cellsco-cultivated with 50 μL of an Agrobacterium strain harboring pDAB1600(donor DNA) and 250 μL of an Agrobacterium strain harboring pDAB4359(C3H Scd27a ZFP-Fok1). Following co-cultivation using the methodsdescribed above, the cells were plated out on the LS-based basal mediumcontaining 500 mg/L carbenicillin and 15 mg/L Bialaphos®. IndividualBialaphos®-resistant isolates appeared 2-4 weeks after plating and weretransferred to individual 60×20 mm plates (one isolate per plate) wherethey were maintained as callus on a 14-day subculture schedule untilneeded for analysis.

Multiple Bialaphos®-resistant isolates were obtained from both C3H IL-1zinc finger nuclease (pDAB4356) and C3H Scd27 zinc finger nuclease(pDAB4359). These isolates were analyzed by PCR using primer pairP24/25, which amplified a DNA fragment spanning the reconstituted PATgene. Primer P24 was homologous to the 5′ end of the PAT coding sequencein the donor DNA and primer P25 was homologous to the 3′ end of the PATcoding sequence in the target DNA. A 2.3 kb PCR fragment would result ifthe two partial PAT coding sequences were joined through homologousrecombination. As shown in FIG. 63, a 2.3 kb PCR product was obtainedfrom multiple isolates analyzed. These isolates were obtained from boththe co-transformation of C3H IL-1 zinc finger-Fok1 fusion proteingene/donor DNA and C3H Scd27 zinc finger-Fok1 fusion protein gene/donorDNA. The 2.3 kb PCR products from multiple independent isolatesrepresentative of those derived from both C3H IL-1 zinc finger-Fok1 andC3H Scd27 zinc finger-Fok1 fusion protein gene transformations werepurified from agarose gels and cloned into the pCR2.1 TOPO vector(Invitrogen, Carlsbad, Calif.). The 2.3 kb PCR product inserted in theTOPO vector was then sequenced using the Dye Terminator Cycle SequencingKit (Beckman Coulter). The sequencing results confirmed that all of thePCR products cloned in the TOPO vector contained the recombined sequenceas predicted, including the 5′ and 3′ partial PAT gene sequences withthe intervening A. thaliana 4-CoAS intron-1. These results confirmed thepredicted inter-chromosomal recombination for both strategies tested andexemplified gene targeting via the expression of C3H zinc finger-Fok1fusion protein genes.

Example 13 Identification of Target Gene Sequences in Maize Cell CultureA. Sequence Identification

In this example, DNA sequences for an endogenous maize gene of knownfunction were selected as targets for genome editing using engineeredzinc-finger nucleases. The genomic structure and sequence of this gene,referred to as IPP2-K, which is derived from proprietary maize inbredline 5XH751, has been described in WO2006/029296; the disclosure ofwhich is incorporated by reference.

In particular, the IPP2-K genomic sequence was used to query the TIGRmaize genome database (available on the internet athttp://www.tigr.org/tdb/tgi/maize/) using BLAST algorithms. Severaladditional genomic fragments were identified with segments ofoverlapping homology to IPP2-K, including, but not limited to,accessions AZM515213 and TC311535. Based on the sequence of theseaccessions as well as the IPP2-K sequence, multiple shortoligonucleotides were designed for use as PCR primers using the Primer3program (Rozen, S. and Skaletsky, H. J. (2000) Primer3 on the WWW forgeneral users and for biologist programmers. In: Krawetz S, Misener S(eds.) Bioinformatics Methods and Protocols: Methods in MolecularBiology. Humana Press, Totowa, N.J., pp 365-386; also available on theinternet). These primers include, but are not limited to, the followingforward orientation oligonucleotides:

(SEQ ID NO: 104) 1. 5′-ATGGAGATGGATGGGGTTCTGCAAGCCGC-3′ (SEQ ID NO: 161)2. 5′-CTTGGCAAGGTACTGCGGCTCAAGAAGATTC-3′ (SEQ ID NO: 162) 3.5′-ATGAAGAAAGACAGGGAATGAAGGAC-3′ (SEQ ID NO: 163) 4.5′-ATGAAGAAAGACAGGGAATGAAGGACCGCCAC-3′ (SEQ ID NO: 164) 5.5′-CATGGAGGGCGACGAGCCGGTGTAGCTG-3′ (SEQ ID NO: 165) 6.5′-ATCGACATGATTGGCACCCAGGTGTTG-3′

In addition, the primers include, but are not limited to, the followingreverse orientation oligonucleotides:

(SEQ ID NO: 166) 7. 5′-TTTCGACAAGCTCCAGAAAATCCCTAGAAAC-3′ (SEQ ID NO:167) 8. 5′-ACAAGCTCCAGAAAATCCCTAGAAACAC-3′ (SEQ ID NO: 168) 9.5′-TTCGACAAGCTCCAGAAAATCCCTAGAAACAC-3′ (SEQ ID NO: 169) 10.5′-TGCTAAGAACATTCTTTTCGACAAGCTCC-3′ (SEQ ID NO: 170) 11.5′-GAACATTCTTTTCGACAAGCTCCAGAAAATCC-3′

All oligonucleotide primers were synthesized by and purchased fromIntegrated DNA Technologies (IDT, Coralville, Iowa).

B. Hi II Maize Cell Culture

To obtain immature embryos for callus culture initiation, F₁ crossesbetween greenhouse-grown Hi-II parents A and B (Armstrong, C., Green, C.and Phillips, R. (1991) Maize Genet. Coop. News Lett. 65: 92-93) wereperformed. Embryos of approximately 1.0-1.2 mm in size (˜9-10 days afterpollination), were harvested from healthy ears and surface sterilized byscrubbing with Liqui-Nox® soap, immersed in 70% ethanol for 2-3 minutes,then immersed in 20% commercial bleach (0.1% sodium hypochlorite) for 30minutes.

Ears were rinsed in sterile, distilled water, and the immature zygoticembryos were aseptically excised and cultured on 15Ag10 medium (N6Medium (Chu C. C., Wang C. C., Sun C. S., Hsu C., Yin K. C., Chu C. Y.,and Bi F. Y. (1975) Sci. Sinica 18:659-668), 1.0 mg/L 2,4-D, 20 g/Lsucrose, 100 mg/L casein hydrolysate (enzymatic digest), 25 mML-proline, 10 mg/L AgNO₃, 2.5 g/L Gelrite, pH 5.8) for 2-3 weeks withthe scutellum facing away from the medium. Tissues showing the expectedmorphology (Welter, M E, Clayton, D S, Miller, M A, Petolino, J F.(1995) Plant Cell Rep: 14:725-729) were selectively transferred atbiweekly intervals onto fresh 15Ag10 medium for approximately 6 weeks,then transferred to 4 medium (N6 Medium, 1.0 mg/L 2,4-D, 20 g/L sucrose,100 mg/L casein hydrolysate (enzymatic digest), 6 mM L-proline, 2.5 g/LGelrite, pH 5.8) at bi-weekly intervals for approximately 2 months.

To initiate embryogenic suspension cultures, approximately 3 ml packedcell volume (PCV) of callus tissue originating from a single embryo wasadded to approximately 30 ml of H9CP+ liquid medium (MS basal saltmixture (Murashige T., & Skoog F. (1962) Physiol. Plant. 15:473-497),modified MS Vitamins containing 10-fold less nicotinic acid and 5-foldhigher thiamine-HCl, 2.0 mg/L 2,4-D, 2.0 mg/L α-naphthaleneacetic acid(NAA), 30 g/L sucrose, 200 mg/L casein hydrolysate (acid digest), 100mg/L myo-inositol, 6 mM L-proline, 5% v/v coconut water (added justbefore subculture), pH 6.0). Suspension cultures were maintained underdark conditions in 125 ml Erlenmeyer flasks in a temperature-controlledshaker set at 125 rpm at 28° C. During cell line establishment (2-3months), suspensions were subcultured every 3.5 days by adding 3 ml PCVof cells and 7 ml of conditioned medium to 20 ml of fresh H9CP+ liquidmedium using a wide-bore pipette. Upon reaching maturity, as evidencedby growth doubling, suspensions were scaled-up and maintained in 500 mlflasks whereby 12 ml PCV of cells and 28 ml conditioned medium wastransferred into 80 ml H9CP+ medium. Upon complete establishment of thesuspension culture, aliquots were cryopreserved for future use. See, WO2005/107437.

C. DNA Isolation and Amplification

Maize HiII cell cultures as described above were grown in 250 ml flasksin standard GN6 medium (N6 medium, 2.0 mg/L 2,4-D, 30 g/L sucrose, 2.5g/L Gelrite, pH 5.8) and genomic DNA was extracted using the Qiagen(Valencia, Calif.) Plant DNeasy extraction kit as per the manufacturer'srecommendations. PCR amplification reactions using the primers describedabove in all possible combinations was carried out under the followingconditions: 25 ul reaction volume containing 20 ng gDNA template, 20pmol each primer, 1% DMSO and 10 units Accuprime™ Pf polymerase(Invitrogen, Carlsbad, Calif.) in the enzyme manufacturer's buffer.Amplification products ranging in size from 500 bp to 2 kb resulted fromamplification cycles consisting of 95oC-1′, (95° C.-30″, 57-62° C.-30″,72° C.-1′) X 30, 72° C.-5′, 4° C-hold. The amplified fragments weredirectly cloned into vector pCR2.1 (Invitrogen, Carlsbad, Calif.) usingthe TA cloning kit from Invitrogen (Carlsbad, Calif.) as per themanufacturer's recommendations.

D. Sequence Analysis

Previous analysis of the IPP2-K gene in maize inbred 5XH751 and HiIIcell culture had indicated the presence of 2-3 distinct genes comprisinga small gene family (Sun et al., in press, Plant Physiology;WO2006029296). Therefore, isolated cloned fragments were sequenced withthe CEQ Dye Terminator Cycle Sequencing Kit from Beckman Coulter(Fullerton, Calif.) as per the manufacturer's recommendations. Sequenceanalysis of multiple clones revealed that 2 distinct gene fragments,derived from 2 distinct and previously characterized loci of the maizegenome, had been isolated from HiII cells.

Comparison of the 2 sequences isolated from HiII cultured cellsindicated that, in predicted coding regions, small differences such assingle nucleotide polymorphisms (SNPs) exist between the 2 paralogs,whereas the intronic and non-coding regions vary significantly at thenucleotide level. These differences between the 2 paralogs are notedbecause they highlight regions of sequence that may be discriminated bya sequence-dependent DNA binding protein such as a zinc-finger domain.One skilled in the art may design zinc-finger DNA binding domains thatbind to one gene sequence and not another, highly similar gene sequence.Partial gene sequence of 1.2 kb corresponding to the paralog of interest(FIG. 66) was selected as template for zinc-finger nuclease proteindesign and subsequently subjected to zinc-finger DNA binding domainanalysis described above.

Example 14 Design of IPP2-K Zinc-Finger DNA Binding Domains

Using target sites identified for IPP2-K, recognition helices wereselected for IPP2-K zinc fingers. The zinc finger designs are shownbelow in Table 8:

TABLE 8 IPP2-K Zinc finger Designs ZFN Name F1 F2 F3 F4 F5 F6 IPP2-DRSALSR RNDDRKK RSDNLST HSHARIK RSDVLSE QSGNLAR K- (SEQ D (SEQ ID (SEQID (SEQ ID (SEQ ID (SEQ ID 1072a1 NO: 105) NO: 106) NO: 107) NO: 108)NO: 109) NO: 110) IPP2- DRSALSR RNDDRKK RSDNLAR TSGSLTR RSDVLSE QSGNLARK- (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID 1072b1 NO: 105) NO:106) NO: 111) NO: 112) NO: 109) NO: 110) IPP2- DRSALSR RNDDRKK TSGNLTRTSGSLTR RSDVLSE QSGNLAR K- (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQID 1072c1 NO: 105) NO: 106) NO: 113) NO: 112) NO: 109) NO: 110) IPP2-RSDHLSE QSATRKK ERGTLAR RSDALTQ NONE NONE K- (SEQ ID (SEQ ID (SEQ ID(SEQ ID r1065a1 NO: 114) NO: 115) NO: 116) NO: 117) IPP2- RSDSLSARSAALAR RSDNLSE ASKTRTN DRSHLAR NONE K- (SEQ ID (SEQ ID (SEQ ID (SEQ ID(SEQ ID r1149a2 NO: 118) NO: 119) NO: 120) NO: 121) NO: 122) IPP2-RSDHLST QSGSLTR RSDHLSE QNHHRIN TGSNLTR DRSALAR K- (SEQ ID (SEQ ID (SEQID (SEQ ID (SEQ ID (SEQ ID 1156a2 NO: 123) NO: 124) NO: 114) NO: 125)NO: 126) NO: 127)

TABLE 9 Target Sites of IPP2-K Zinc Fingers Target sites of the zincfinger designs are shown below in Table 9: ZFN Name Target Site (5′ to3′) IPP2-K-1072a1 GAACTGGTTGAGTCGGTC (SEQ ID NO: 128) IPP2-K-1072b1GAACTGGTTGAGTCGGTC (SEQ ID NO: 129) IPP2-K-1072c1 GAACTGGTTGAGTCGGTC(SEQ ID NO: 129) IPP2-K-r1065a1 ATGGCCCCACAG (SEQ ID NO: 130)IPP2-K-r1149a2 GGCACCCAGGTGTTG (SEQ ID NO: 131) IPP2-K-1156a2GTCGATGGTGGGGTATGG (SEQ ID NO: 132)

The IPP2-K designs were incorporated into zinc finger expression vectorsencoding a protein having a CCHC structure. See, Tables 1 through 4above. The non-canonical zinc finger-encoding sequences were then fusedto the nuclease domain of the type IIS restriction enzyme FokI (aminoacids 384-579 of the sequence of Wah et al. (1998) Proc. Natl. Acad.Sci. USA 95:10564-10569 via a four amino acid ZC linker) to form IPP2-KZFNs.

Example 15 Gene Correction using IPP2-K Zinc-Finger Nucleases

The ability of IPP2-K ZFNs as described herein to facilitate homologousrecombination was tested in the GFP system described in Urnov (2005)Nature 435(7042):646-51 and U.S. Patent Publication No. 20050064474(e.g., Examples 6-11). Briefly, 50 ng of each ZFN and 500 ng of thepromoter-less GFP donor (Urnov (2005) Nature) were transfected into500,000 reporter cells, using 2 uL of Lipofectamine 2000 per sample, asper the Invitrogen Lipofectamine 2000 protocol.

Vinblastine was added 24 hours post-transfection at a 0.2 uM finalconcentration, and was removed 72 hours post-transfection.

The cells were assayed for GFP expression 5 days post-transfection bymeasuring 40,000 cells per transfection on the Guava benchtop FACSanalyzer. Results are shown in FIG. 69.

Example 16 Expression C3H1 ZFNs in Maize HiII Cells A. Vector Design

Plasmid vectors for the expression of ZFN proteins in maize cells wereconstructed. In order to optimize the expression and relativestoichiometry of the 2 distinct proteins required to form a functionalzinc-finger nuclease heterodimer, an expression strategy was adoptedthat results in insertion of the open reading frames of both ZFNsmonomers on a single vector, driven by a single promoter. This strategyexploits the functionality of a 2A sequence (Mattion, N. M., Harnish, E.C., Crowley, J. C. & Reilly, P. A. (1996)J. Virol. 70, 8124-8127)derived from the Thesoa assigna virus, a maize nuclear localization(NLS) signal from the opaque-2 gene (op-2) (Maddaloni, M., Di Fonzo, N.,Hartings, H., Lazzaroni, N., Salaminil, F., Thompson, R., & Motto M.(1989) Nucleic Acids Research Vol. 17(18):7532), and a promoter derivedfrom the maize ubiquitin-1 gene (Christensen A. H., Sharrock R. A., &Quail P. H. (1992) Plant Mol Biol. 18(4):675-89). A stepwise modularcloning scheme was devised to develop these expression vectors for anygiven pair of ZFN-encoding genes selected from the library archive orsynthesized de novo.

First, a pVAX vector (see, for example U.S. Patent Publication2005-0267061; the disclosure of which is incorporated by reference) wasmodified to encompass the N-terminal expression domain as shown in FIG.65, panels A to E. Features of this modified plasmid(pVAX-N2A-NLSop2-EGFP-FokMono) (FIG. 65A) include a redesigned andsynthesized segment encoding a NLS derived from maize op-2(RKRKESNRESARRSRYRK, SEQ ID NO:133), and a redesigned and synthesizedsegment encoding the FokI nuclease domain utilizing the maizecodon-bias. Additionally, a single nucleotide insertion (C) downstreamof the unique XhoI site created an extra SacI site for cloningconvenience.

Second, a pVAX vector (see, for example U.S. Patent Publication2005-0267061) was also modified to encompass the C-terminal expressiondomain. Features of this modified plasmid (pVAX-C2A-NLSop2-EGFP-FokMono)(FIG. 65B) include a redesigned and synthesized segment encoding a NLSderived from maize op-2 (RKRKESNRESARRSRYRK, SEQ ID NO:133), and aredesigned and synthesized segment encoding the FokI nuclease domainutilizing the maize codon-bias. Additionally, the 2A sequence fromThosea asigna virus (EGRGSLLTCGDVEENPGP, SEQ ID NO:134) was introducedat the N-terminus of the ZFN ORF for the purpose of subsequent linkingof the 2 protein encoding domains.

The gene cassettes encoding the ORFs of individual zinc-finger proteinswere cloned into either the N2A or C2A vector via ligation using therestriction enzymes KpnI and BamHI to create compatible ends. Next, theBg1II/XhoI fragment from the C2A vector was inserted into the N2A vectorvia the same restriction sites, yielding an intermediate construct thatcontains a cassette including 2 ZFN-encoding domains flanked by NcoI andSacI restriction sites.

Finally, the NcoI/SacI cassette from this intermediate construction(FIG. 65C), containing both ZFN genes, was excised via restriction usingthose enzymes and ligated into the plasmid backbone pDAB3872 (FIG. 65D).The resulting plasmids include the ZFN genes plus the relevant promoterand terminator sequences, plus selectable markers for plasmidmaintenance.

In the final constructions, an example of which is shown in FIG. 65E,the ZFN expression cassette (including promoter and terminator elements)is flanked by attL sites for convenient manipulation using the Gatewaysystem from Invitrogen (Carlsbad, Calif.). Each of the ZFN constructsgenerated using this cloning scheme were transformed into E. coli DH5acells (Invitrogen, Carlsbad, Calif.) and subsequently maintained underthe appropriate selection.

B. DNA Delivery and Transient Expression

Plasmid preparations of ZFN expression vectors constructed as describedin FIG. 65E were generated from 2 L cultures of E. coli cells grown inLB media plus antibiotics using an Endonuclease-free Gigaprep kit fromQiagen (Valencia, Calif.) as per the manufacturer's recommendations.Plasmid DNA was delivered directly to maize HiII culture cells using avariety of methods.

In one example, maize cells were subjected to DNA delivery viaWhiskers™. Approximately 24 hours prior to DNA delivery, 3 ml PCV ofHiII maize suspension cells plus 7 ml of conditioned medium wassubcultured into 20 ml of GN6 liquid medium (GN6 medium lacking Gelrite)in a 125 ml Erlenmeyer flask, and placed on a shaker at 125 rpm at 28°C. for 24 hours. 2 mL PCV was removed and added to 12 ml GN6 S/M osmoticmedium (N6 Medium, 2.0 mg/L 2,4-D, 30 g/L sucrose, 45.5 g/L sorbitol,45.5 g/L mannitol, 100 mg/L myo-inositol, pH 6.0) in a 125 mL Erlenmeyerflask. The flask was incubated in the dark for 30-35 minutes at 28° C.with moderate agitation (125 rpm). During this time a 50 mg/mlsuspension of silicon carbide whiskers (Advanced Composite Materials,Inc., Eureka Springs, Ak.) was prepared by adding the appropriate volumeof GN6 S/M liquid medium to pre-weighed sterile whiskers. Followingincubation in GN6 S/M, the contents of each flask were poured into a 15mL conical centrifuge tube.

After the cells settled, all but 1 mL of GN6 S/M liquid was drawn offand collected in the 125 mL flask for future use. The pre-wettedsuspension of whiskers was vortexed for 60 seconds on maximum speed, 160μL was added to the centrifuge tube using a wide-bore, filtered pipettip, and 20 μg DNA was added. The tube was ‘finger vortexed,’ andimmediately placed in a Caulk ‘Vari-Mix II’ dental amalgamator, modifiedto hold a 17×100 mm culture tube, and then agitated for 60 seconds onmedium speed. After agitation, the cocktail of cells, media, whiskersand DNA was returned to the Erlenmeyer flask along with 18 ml ofadditional GN6 liquid medium. The cells were allowed to recover on ashaker at 125 RPM for 2 hours at 28° C. in the dark.

Approximately 5-6 mL of dispersed suspension was filtered onto Whatman#4 filter paper (5.5 cm) using a glass cell collector unit connected toa house vacuum line such that 5-6 filters were obtained per sample.Filters were placed onto 60×20 mm plates of GN6 medium and cultured at28° C. under dark conditions. After 24, 48, or 72 hours, the cells from2-5 filter papers were scraped off, collected into a tube, placed on dryice, and then frozen at −80° C.

In another example of DNA delivery, the purified endonuclease-freeplasmid preparations were delivered directly to maize cells usingmicro-projectile bombardment techniques adapted from the instrumentmanufacturer's protocol. All bombardments were conducted with theBiolistic PDS-1000/He™ system (Bio-Rad Laboratories, Hercules, Calif).For particle coating, 3 mg of 1.0 micron diameter gold particles werewashed once with 100% ethanol, twice with sterile distilled water andresuspended in 50 μl water in a siliconized Eppendorf tube. Fivemicrograms of plasmid DNA, 20 μl spermidine (0.1 M) and 50 μl calciumchloride (2.5 M) were added to the gold suspension. The mixture wasincubated at room temperature for 10 min, pelleted at 10K rpm for 10s,resuspended in 60 μl cold 100% ethanol and 8-9 μl was distributed ontoeach macrocarrier. To prepare the cells for bombardment, cell clusterswere removed from liquid culture 3 days post-subculture and placed on acircle 2.5 cm in diameter of osmotic medium consisting of growth mediaplus 0.256 M each of mannitol and sorbitol in a Petri dish. The cellswere incubated in osmoticum for 4 h prior to bombardment. Bombardmenttook place in the instrument described above using by placing the tissueon the middle shelf under conditions of 1100 psi and 27 in of Hg vacuumand following the operational manual. At a time point of 24 hourspost-treatment, the bombarded cell clusters were harvested, frozen inliquid N₂ and stored at −80° C.

Another example of DNA delivery and transient expression of ZFNs inmaize cells involved the utilization of protoplast preparations. Usingmethods modified from Mitchell and Petolino (1991) J. Plant. Physiol.137: 530-536 and Lyznik et al. (1995) Plant J. 8(2): 177-186),protoplasts were prepared from HiII maize cell culture. Suspensioncultures were harvested 48 hours post-subculture (mid-log growth) bycentrifugation at 1000 rpm for 5 minutes. Culture medium was removed and5 ml packed PCV was gently washed in 10 ml W5 medium (154 mM NaCl₂; 125mM CaCl₂H₂O; 5 mM KCl₂; 5 mM glucose; pH 5.8).

Washed cells were collected via centrifugation at 100 rpm for 5 minutesand subsequently incubated in an enzymatic cocktail containing 3%Cellulase Y-C+0.3% pectolyase Y23 (Karlan Research Products Corp.,Cottonwood, Ariz.) in 25 ml of filter sterilized K3 medium (2.5 g KNO₃;250 mg NH₄NO₃; 900 mg CaCl₂ (dihydrate); 250 mg Mg₂SO₄; 250 mg NH₄SO₄;150 mg NaPO₄ (monobasic); 250 mg xylose; 10 ml ferrous sulfate/chealatestock (F318); 1 ml B5 micronutrient (1000× stock-750 mg potassiumiodide; 250 mg molybdic acid (sodium salt) dehydrate; 25 mg cobaltchloride; 25 mg cupric sulfate); 10 ml K3 Vitamins (100× stock-1 gmyo-inositol; 10 mg pyridoxine HCl; 100 mg thiamine HCl; 10 mg nicotincacid);+0.6M mannitol; pH=5.8]. Cells were incubated at 25° C. for 5-6hours with gentle agitation (50 rpm) in order to digest the secondaryplant cell wall.

Upon degradation of the cell wall, the enzyme-cell mixture was filteredthrough a 100 micron cell strainer and the flow-through, containingprotoplasts and cell debris, was washed with an equal volume of K3+0.6Mmannitol medium. The protoplasts were centrifuged at 800 rpm for 5minutes, the supernatant was discarded and the washing was repeated. Theprotoplast pellet was washed resuspended in 20 ml K3+0.6M mannitol +9%Ficoll 400 solution. Ten ml of this solution was dispensed into 2sterile plastic tubes and 2 ml of TM medium (19.52 g MES; 36.45 gmannitol; 40 ml 2M CaCl₂H₂O stock; pH=5.5)) was gently overlaid on thesuspension, forming a discontinuous gradient.

Viable protoplasts were separated from non-viable protoplast, celldebris and intact suspension cells via centrifugation at 800 rpm for 5minutes. The distinct protoplast band formed at the gradient interfacewas removed with a pipette and washed with 10 ml fresh TM solution,followed by centrifugation at 800 rpm for 5 minutes. The resultingprotoplast pellet was re-suspended in 1 ml of TM medium and the numberof viable protoplasts was quantitated with 25 mg/mg fluoresceindiacetate (FDA) staining in a hemocytometer. The protoplast solution wasadjusted to a final concentration to 1×10⁷ protoplasts/ml in TM medium.

Approximately 1×10⁶ protoplasts (100 μl) were transferred to a 2 mlEppendorf tube containing 10-80 μg purified plasmid DNA. 100 μl of a 40%PEG-3350 (Sigma Chemical Co., St. Louis, Mo.) solution was addeddrop-wise and the suspension was gently mixed. The protoplast/DNAmixture was incubated for 30 minutes at room temperature, followed by adrop-wise dilution with 1 ml GN6 growth medium. The diluted protoplastswere incubated in this medium for 24 hours at 25° C. and subsequentlyharvested, frozen in liquid N₂ and stored at −80° C.

Example 17 In Vivo ZFN Functionality

Functionality of a ZFN in this example is understood to include (but notbe limited to) the ability of a ZFN to express in cells of a cropspecies, and for that ZFN to mediate a double stranded break in theendogenous genome of that crop through recognition of, binding to andcleavage of its desired target. It is also understood that, in thisexample, the target of the ZFN is a gene in an endogenous locus andconformation within the crop genome.

In order to assess whether engineered ZFNs have functionality againstthe predicted target gene in a genomic context, DNA-sequence basedassays were deployed. ZFN-induced double-stranded DNA breaks arepredicted to induce repair mechanisms such as non-homologous end-joining(NHEJ) (reviewed by Cahill et al., (2006) Mechanisms Front Biosci.1(11): 1958-76). One outcome of NHEJ is that a proportion of the brokenDNA strands will be repaired in an imperfect manner, resulting in smalldeletions, insertions or substitutions at the cleavage site. One skilledin the art may detect these changes in DNA sequence through a variety ofmethods.

A. PCR-Based Cloning and Sequencing

In one example, maize HiII cultured cells expressing ZFN proteins wereisolated at 24 hours post-transformation, frozen and subjected togenomic DNA extraction using the Qiagen (Valencia, Calif.) Plant DNeasyextraction kit as per the manufacturer's recommendations. PCRamplification was carried out using oligonucleotide primers specific forthe target gene and flanking the predicted cleavage site of the ZFN. Aforward orientation PCR primer (5′-GGAAGCATTATTCCAATTTGATGATAATGG-3′)(SEQ ID NO:135) and reverse orientation PCR primer(5′-CCCAAGTGTCGAGGTTGTCAATATGTTAC-3′) (SEQ ID NO:136) specific for thetargeted IPP2-K gene paralog were used in combination to amplifypurified genomic DNA under the following conditions: 25 ul reactionvolume containing 20 ng gDNA template, 20 pmol each primer, 1% DMSO and10 units Accuprime Pf polymerase (Invitrogen, Carlsbad, Calif.) in theenzyme manufacturer's buffer. Amplification products of the expectedsize resulted from amplification cycles consisting of 95° C.-1′, (95°C.-30″, 61° C.-30″, 72° C.-1′) X 30, 72° C.-5′, 4° C.-hold.

The amplified fragments were directly cloned into vector pCR2.1(Invitrogen, Carlsbad, Calif.) using the TA cloning kit from Invitrogen(Carlsbad, Calif.). Isolated cloned fragments were sequenced with theCEQ Dye Terminator Cycle Sequencing Kit from Beckman Coulter (Fullerton,Calif.) as per the manufacturer's recommendations in a 96-well format.In this experiment, the ZFN proteins are predicted to bind to 2 shortIPP2-K gene-specific sequences to create a heterodimeric nuclease thatcleaves the ds-DNA as shown in FIG. 66.

Analysis of sequencing results from multiple clones revealed that clone#127 contained a small deletion at precisely the predicted cleavage siteof the ZFN, indicating that the NHEJ mechanism had mediated an imperfectrepair of the DNA sequence at that site (FIG. 67).

These results demonstrate the ability of these engineered ZFNs to inducetargeted, double stranded breaks in a specific manner at an endogenousgene locus within a crop species.

B. Massively Parallel Sequencing Analysis

In another example, a combination of PCR and massively-parallelpyrosequencing methods were applied to interrogate the genomes ofmultiple cell samples expressing different ZFN proteins targeted againstthis same sequence. Three variants of a forward orientation PCR primer(5′-XXXCACCAAGTTGTATTGCCTTCTCA-3′) (SEQ ID NO:137) in which XXX=GGG,CCC, or GGC and three variants of a reverse orientation PCR primer(5′-XXXATAGGCTTGAGCCAAGCAATCTT-3′) (SEQ ID NO:138) in which XXX=GCC, CCGor CGG were synthesized (IDT, Coralville, Iowa). The 3-bp tags at the5′-end of each primer serve as an identifier key and indicate which cellsample the amplicon originated from. Primer pairs with matchingidentifier tags (keys) were used in combination to amplify purifiedgenomic DNA derived from maize cell samples under the followingconditions: 50 ul reaction volume containing 40 ng gDNA template, 20pmol each primer, 1% DMSO and 10 units Accuprime Pf polymerase(Invitrogen, Carlsbad, Calif.) in the enzyme manufacturer's buffer.Amplification products of the expected size resulted from amplificationcycles consisting of 95° C.-1′, (95° C.-30″, 65° C.-30″, 72° C.-1′) X30, 4° C.-hold and were purified using Qiagen's (Valencia, Calif.)MinElute PCR purification kit as per the manufacturer's recommendations.

Massively parallel pyrosequencing reactions (also known as 454sequencing) were performed directly on PCR products as described in(Margulies et al. (2005) Nature 437: 376-380) by 454 Life Sciences(Branford, Conn.). Analysis of 454 sequencing results was carried out byidentifying sequence reads containing deletions of the expected size andposition within the DNA molecule.

Results of these analyses indicated the presence of multiple smalldeletions at the expected cleavage site for these ZFNs, as shown in FIG.68. These deletions are precisely localized to the ZFN target site andindicate that ds breaks, induced by the ZFN, were generated in thegenome and subsequently repaired by NHEJ. These results furtherdemonstrate the ability of these engineered ZFNs to induce targeted,double stranded breaks in a specific manner at an endogenous gene locuswithin a crop species.

Example 18 Donor DNA Design for Targeted Integration

In this example, donor DNA is understood to include double-stranded DNAmolecules that are delivered into plant cells and incorporated into thenuclear genome. The mechanism by which this incorporation takes placemay be via homology-independent non-homologous end joining (NHEJ;reviewed by Cahill et al., (2006) Mechanisms Front Biosci. 1: 1958-76)or another similar mechanism at the site of a double stranded break inthe nuclear DNA. Such NHEJ-driven, ligation-like incorporation of donorDNA into the genome is referred to as random integration, since theintegration position of the donor DNA is primarily determined by thepresence of a double stranded DNA break. In this mechanism, donor DNAintegration into the genome is not dependent on either the nucleotidesequence of the genome at the site of the break or the nucleotidesequence of the donor itself. Therefore, during random integration, the“address” in the genome at which the donor DNA is incorporated is notspecified nor predicted based on the sequence of the donor DNA. Randomintegration is the primary mechanism by which transgenesis of donor DNAoccurs during standard plant transformation via either Agrobacterium- orbiolistic-mediated DNA delivery into living plant cells.

In contrast to random integration, donor DNA may also incorporate intothe genome via targeted integration. Targeted integration is understoodto occur at the site of a double-stranded break (position) viahomology-dependent mechanisms such as homology-dependent single strandedannealing or homologous recombination (reviewed in van den Bosch et al.(2002) Biol Chem. 383(6): 873-892). In the case of homology-dependentDNA break repair, donor DNA that contains nucleotide sequence withidentity or similarity to the DNA at the break site may incorporate atthat site. Therefore, the “address” at which the donor DNA integratesinto the genome is dependent on nucleotide sequence identity or sequencesimilarity between the genome and donor DNA molecules. In plant systems,repair of double-stranded breaks in DNA is known to utilize both NHEJand homology-dependent pathways (reviewed in Puchta (2005) J. Exp. Bot.56: 1-14).

In this example, we describe the design and construction of donor DNAmolecules to be integrated into the genome via targeted integration atthe site of a double stranded break induced by sequence-specific ZFNproteins. Different ZFN proteins may induce double-stranded breaks atdifferent nucleotides in the target gene sequence; the specific site ofthe induced double stranded break is referred to as the position.

As described in Example 13, we have characterized the nucleotidesequence of a target gene, IPP2K from maize. Subsequently, we designedZFN proteins to bind to specific bases of that target gene (Example 14)and validated their binding/cleavage activity at that sequence withinthe target gene in both heterologous systems and against the endogenousgene in maize cells (Examples 15-17). Here, we describe the constructionof various donor molecules designed to incorporate into the maize genomeat the position of the ZFN-mediated double stranded break in the IPP2Kgene via targeted integration. One skilled in the art might construct adonor DNA molecule designed to incorporate into a ZFN-induced doublestranded break via homology-driven targeted integration at any positionin any genome for which nucleotide sequence is known and that sequenceis predicted to contain a double stranded break.

In one embodiment described herein, the donor DNA molecule comprises anautonomous herbicide-tolerance gene expression cassette bounded bysegments of nucleotide sequence identical to that of the target gene,IPP2K at the targeted position. In this embodiment, the autonomousherbicide tolerance cassette is understood to include a completepromoter-transcription unit (PTU) containing a promoter, herbicidetolerance gene, and terminator sequence known to be functional in plantcells. One skilled in the art may select any promoter, gene andterminator combination to constitute the autonomous PTU. Also includedon this plasmid construct are DNA fragments with sequence identity tothe target gene in maize (IPP2K) at the position indicated. Thesefragments serve as the “homology flanks” of the donor DNA and directincorporation of this donor into the target gene at the specifiedposition via targeted integration. The homology flanks are placed bothupstream and downstream of the PTU in the correct 5′- to 3′-orientationrelative to the PTU. One skilled in the art may envision homology flanksof varying size and orientation in a donor DNA construction.

In another embodiment described herein, the donor DNA molecule comprisesa plasmid construction containing a non-autonomous herbicide-tolerancegene expression cassette bounded by segments of nucleotide sequenceidentical to that of IPP2K at the target position. In this embodiment,the non-autonomous herbicide tolerance cassette is understood to includean incomplete promoter-transcription unit (PTU) that lacks a functionalpromoter. The non-autonomous PTU does contain an herbicide tolerancegene, and terminator sequence known to be functional in plant cells. Oneskilled in the art may select any gene and terminator combination toconstitute a non-autonomous PTU. In this example of a non-autonomousdonor, expression of the herbicide tolerance gene is dependent onincorporation of the donor segment into a genomic location proximal to afunctional promoter that may drive expression of that gene. One mightenvision the relatively rare situation in which the donor willincorporate via random integration into a genetic locus where aserendipitous promoter resides and is available to drive expression ofthe herbicide tolerance gene. Alternatively, based on the presence ofhomology flanks of DNA fragments of the appropriate length with sequenceidentity to the target gene at a specified position in maize within thedonor DNA construction, precise targeted integration of the donor DNAinto the target gene at the specified position may occur (as describedfor the autonomous donor) and therefore exploit the endogenous promoterof said target gene. In this embodiment, the homology flanks are placedboth upstream and downstream of the PTU in the correct 5′- to3′-orientation relative to the PTU. One skilled in the art may envisionhomology flanks of varying size and orientation in a donor DNAconstruction.

In both embodiments described herein (autonomous and non-autonomousdonor design), the plasmid constructions typically contain additionalelements to enable cloning, expression of the herbicide tolerance gene,and subsequent analysis. Such elements include bacterial origins ofreplication, engineered restriction sites, etc. and are described below.One skilled in the art may envision the utilization of differentelements comprising a donor DNA molecule.

A. Bacterial Strains and Culture Conditions

Escherichia coli strains (One Shot® Top 10 Chemically Competent Cells;MAX Efficiency® DH5α™ Chemically Competent Cells, Invitrogen LifeTechnologies, Carlsbad, Calif.), were grown at 37° C., 16 hrs usingLuria-Bertani broth (LB: 10 g/L Bacto-tryptone, 10 g/L NaCl, 5 g/LBacto-yeast extract), LB agar (LB broth plus 15 g/L Bacto-agar), orTerrific broth (TB: 12 g/L Bacto-tryptone, 24 g/L Bacto-yeast extract,0.4% v/v glycerol, 17 mM KH₂PO₄, 72 mM K₂HPO₄). Liquid cultures wereshaken at 200 rpm. Chloramphenicol (50 μg/ml), kanamycin (50 μg/ml), orampicillin (100 μg/ml) were added to the media as required. Allantibiotics, culture media and buffer reagents used in this study werepurchased from Sigma-Aldrich Corporation (St. Louis, Mo.) or DifcoLaboratories (Detroit, Mich.).

B. Plasmid Backbone Position-1

A plasmid backbone containing homology flanks for position-1 of IPP2Kwas engineered to allow for the integration of any donor DNA sequenceinto the corresponding target site of the IPP2K gene. One skilled in theart may envision plasmid backbones using various cloning sites, modulardesign elements and sequence homologous to any target sequence withinthe genome of interest. The plasmid backbone exemplified here originatedwith the base plasmid vector pBC SK(−) phagemid (3.4 Kbp) (Stratagene,La Jolla, Calif.). A four-step synthesis as described below was used toconstruct the position-1 plasmid backbone.

In step #1, the base plasmid was prepared. Three μg pBC SK(−) werelinearized using 10 units of Spe I and 10 units of Not I (New EnglandBiolabs, Beverly, Mass.) restriction endonucleases for 1 hr at 37° C.Restricted DNA was electrophoresed at 100 V for 1 hr in a 1.0% TAE (0.04M Tris-acetate, 0.002 M EDTA) agarose gel supplemented with 0.5%ethidium bromide (Sigma-Aldrich Corporation, St. Louis, Mo.). DNAfragments were visualized with UV light and fragment size estimated bycomparison with 1 Kbp DNA ladder (Invitrogen Life Technologies,Carlsbad, Calif.). The 3.4 Kbp Spe I/Not I digested subdloning vector,pBC SK(−) was gel-excised and purified according to the manufacturer'sdirections using QIAquick Gel Extraction Kit (QIAGEN Inc., Valencia,Calif.).

In step#2, 5′- & 3′-homology flanks from IPP2K position-1 were isolated.The following oligonucleotide primers were synthesized by Integrated DNATechnologies, Inc. (Coralville, Iowa) under conditions of standarddesalting and diluted with water to a concentration of 0.125 μg/ul:

(SEQ ID NO: 143) 5′- GCGGCCGCGTCTCACCGCGGCTTGGGGATTGGATACGGAGCT -3′ (SEQID NO: 144) 5′- ACTAGTGATATGGCCCCACAGGAGTTGCTCATGACTTG -3′ (SEQ ID NO:145) 5′- ACTAGTCCAGAACTGGTTGAGTCGGTCAAACAAGATTGCT -3′ (SEQ ID NO: 146)5′- GTCGACCTTGATGCTACCCATTGGGCTGTTGT -3′

PCR amplification reactions were carried out using reagents provided byTaKaRa Biotechnology Inc., Seta 3-4-1, Otsu, Shiga, 520-2193, Japan andconsisted of the following: Five μl 10× LA PCR™ Buffer II (Mg2⁺), 20 ngdouble-stranded gDNA template (maize HiII), 10 pmol forwardoligonucleotide primer, 10 pmol reverse oligonucleotide primer, 8 μldNTP mix (2.5 mM each), 33.5 μl H₂O, 0.5 μl (2.5 units) TaKaRa LA Taq™DNA polymerase, 1 drop of mineral oil. PCR reactions were performedusing a Perkin-Elmer Cetus, 48-sample DNA Thermal Cycler (Norwalk,Conn.) under the following cycle conditions: 94° C., 4 min/1 cycle; 98°C. 20 sec, 65° C. 1 min, 68° C. 1 min/30 cycles; 72° C., 5 min/1 cycle;4°/hold. Fifteen μl of each PCR reaction was electrophoresed at 100 Vfor 1 hr in a 1.0% TAE agarose gel supplemented with 0.5% ethidiumbromide. Amplified fragments were visualized with UV light and fragmentsize estimated by comparison with 1 Kbp DNA ladder. Expectedamplification products were diagnosed by the presence of either a DNAfragments of 0.821 Kbp (5′-homology flank) or 0.821 Kbp (3′-homologyflank).

These fragments were gel-excised and purified according tomanufacturer's directions using QIAquick Gel Extraction Kit (QIAGENInc., Valencia, Calif.). Purified fragments were then cloned into pCR2.1plasmid using TOPO TA Cloning® Kit (with pCR® 2.1 vector) and One Shot®TOP10 Chemically competent E. coli cells (Invitrogen Life Technologies,Carlsbad, Calif.) according to manufacturer's protocol.

Individual colonies were inoculated into a 14 ml Falcon Tube(Becton-Dickinson, Franklin Lakes, N.J.) containing 2 ml TB supplementedwith 50 μl/ml kanamycin and incubated for 16 hrs at 37° C. with shakingat 200 rpm. Following incubation, 1.5 ml cells were transferred to a 1.7ml Costar microcentrifuge tube (Fisher Scientific, Pittsburgh, Pa.) andpelleted at 16,000×g for 1 min. Supernatant was removed and plasmid DNAwas isolated as described above using NucleoSpin® Plasmid Kit (BDBiosciences/Clontech/Macherey-Nagel, Palo Alto, Calif.). Three μg ofisolated plasmid from 5′-homology flank clone plasmids was digested with10 units Spe I and Not I. Three prime-homology flank clone plasmids weredigested with 10 units Spe I and 20 units Sal I (New England Biolabs,Beverly, Mass.). All plasmid digestions were incubated for 1 hr at 37°C. Restricted DNA was electrophoresed at 100 V for 1 hr in a 1.0% TAEagarose gel supplemented with 0.5% ethidium bromide. Fragments werevisualized with UV light and fragment size estimated by comparison with1 Kbp DNA ladder. Expected plasmid clones were diagnosed by the presenceof inserted DNA fragments of 0.821 Kbp (5′-homology flank) or 0.821 Kbp(3′-homology flank) in addition to the 3.9 Kbp pCR® 2.1 vector.

Double-stranded sequencing reactions of plasmid clones were performed asdescribed by manufacturer using CEQ™ DTCS-Quick Start Kit(Beckman-Coulter, Palo Alto, Calif.). Reactions were purified usingPerforma DTR Gel Filtration Cartridges (Edge BioSystems, Gaithersburg,Md.) as described by manufacturer protocols. Sequence reactions wereanalyzed on a Beckman-Coulter CEQ™ 2000 XL DNA Analysis System andnucleotide characterization performed using Sequencher™ version 4.1.4(Gene Codes Corporation, Ann Arbor, Mich.). The sequence of the 0.821Kbp fragment corresponding to the position-1 5′-homology flank derivedfrom IPP2K is shown in FIG. 87 (SEQ ID NO:171). The sequence of the0.821 Kbp fragment corresponding to the position-1 3′-homology flankderived from IPP2K is shown in FIG. 88 (SEQ ID NO:172).

In step #3 position-1 5′-homology flanks were ligated into the baseplasmid. Restricted fragments corresponding to clones that contained thecorrect position-1 5′-homology flank sequence were gel-excised andpurified according to the manufacturer's directions using QIAquick GelExtraction Kit (QIAGEN Inc., Valencia, Calif.). Fragments correspondingto the position-1 5′-homology flank (0.821 Kbp) were then ligated topurified base plasmid digested with Spe I/Not I (step #1) at a 1:5vector:insert ratio using 500 units T4 DNA Ligase (Invitrogen LifeTechnologies, Carlsbad, Calif.) in a reaction volume of 20 μl underconditions of 16 hr incubation in a 16° C. water bath. Five μl of theligation reaction was subsequently transformed E. coli One Shot® Top 10Chemically Competent Cells, (Invitrogen Life Technologies, Carlsbad,Calif.) and plated under selection conditions described by themanufacturer. Individual colonies were inoculated into a 14 ml FalconTube (Becton-Dickinson, Franklin Lakes, N.J.) containing 2 ml TBsupplemented with 50 μl/ml kanamycin and incubated for 16 hrs at 37° C.shaking 200 rpm.

Following incubation, 1.5 ml cells were transferred to a 1.7 ml Costarmicrocentrifuge tube (Fisher Scientific, Pittsburgh, Pa.) and pelletedat 16,000×g for 1 min. Supernatant was removed and plasmid DNA wasisolated as described above using NucleoSpin® Plasmid Kit (BDBiosciences/Clontech/Macherey-Nagel, Palo Alto, Calif.). Three μg ofisolated plasmid DNA was digested with 10 units Spe I and Not I. (NewEngland Biolabs, Beverly, Mass.) and incubated for 1 hr at 37° C.Restricted DNA was electrophoresed at 100 V for 1 hr in a 1.0% TAEagarose gel supplemented with 0.5% ethidium bromide. Fragments werevisualized with UV light and fragment size estimated by comparison with1 Kbp DNA ladder. Expected plasmid clones were diagnosed by the presenceof an inserted DNA fragment of 0.821 Kbp (5′-homology flank) in additionto the 3.4 Kbp base plasmid.

In step#4, position-1 3′-homology flanks were ligated into the step #3product. Three μg of the engineering product described in step #3 waslinearized using 10 units of Spe I and 20 units of Sal I (New EnglandBiolabs, Beverly, Mass.) restriction endonucleases for 1 hr at 37° C.Restricted DNA was electrophoresed at 100 V for 1 hr in a 1.0% TAE (0.04M Tris-acetate, 0.002 M EDTA) agarose gel supplemented with 0.5%ethidium bromide (Sigma-Aldrich Corporation, St. Louis, Mo.). DNAfragments were visualized with UV light and fragment size estimated bycomparison with 1 Kbp DNA ladder (Invitrogen Life Technologies,Carlsbad, Calif.). The 4.2 Kbp Spe I/Sal I digested product from step #3was gel-excised and purified according to the manufacturer's directionsusing QIAquick Gel Extraction Kit (QIAGEN Inc., Valencia, Calif.).

Isolated fragments of the 3′-homology flank donor (0.821 Kbp) generatedin step #2 were subsequently combined with step #3 product that wasdigested with Spe I/Sal I and purified as described above in a 20 μlligation reaction using a 1:5 vector:insert ratio and 500 units T4 DNALigase (Invitrogen Life Technologies, Carlsbad, Calif.). Ligationreactions were incubated for 16 hr in a 16° C. water bath. Following theligation, 5 μl of the ligation reaction was transformed into MAXEfficiency® DH5°™ Chemically Competent Cells (Invitrogen LifeTechnologies, Carlsbad, Calif.) as per the manufacturer'srecommendations. Individual colonies inoculated into a 14 ml Falcon Tube(Becton-Dickinson, Franklin Lakes, N.J.) containing 2 ml TB supplementedwith 50 μl/ml chloramphenicol.

Cultures were incubated for 16 hrs at 37° C. shaking 200 rpm. Followingincubation, 1.5 ml cells were transferred to a 1.7 ml Costarmicrocentrifuge tube (Fisher Scientific, Pittsburgh, Pa.) and pelletedat 16,000×g for 1 min. Supernatant was removed and plasmid DNA wasisolated as described above using NucleoSpin® Plasmid Kit (BDBiosciences/Clontech/Macherey-Nagel, Palo Alto, Calif.). Three μgisolated plasmid was digested with 10 units Sal I and Not I. (NewEngland Biolabs, Beverly, Mass.) and incubated for 1 hr at 37° C.Restricted DNA was electrophoresed at 100 V for 1 hr in a 1.0% TAEagarose gel supplemented with 0.5% ethidium bromide. Fragments werevisualized with UV light and fragment size estimated by comparison with1 Kbp DNA ladder. Expected clones were diagnosed by the presence of twoDNA fragments of 1.64 Kbp (insert) and 3.33 Kbp (base plasmid). Theresulting plasmid was given the name pDAB7471 (FIG. 70).

C. Plasmid Backbone Position-2

A plasmid backbone containing homology flanks for position-2 of IPP2Kwas engineered to allow for the integration of any donor DNA sequenceinto the corresponding target site of the IPP2K gene. One skilled in theart may envision plasmid backbones using various cloning sites, modulardesign elements and sequence homologous to any target sequence withinthe genome of interest. The plasmid backbone exemplified here originatedwith the base plasmid vector pBC SK(−) phagemid (3.4 Kbp) (Stratagene,La Jolla, Calif.). A four-step synthesis as described below was used toconstruct the position-2 plasmid backbone.

In step #1, the base plasmid was prepared. Three μg pBC SK(−) werelinearized using 10 units of Spe I and 10 units of Not I (New EnglandBiolabs, Beverly, Mass.) restriction endonucleases for 1 hr at 37° C.Restricted DNA was electrophoresed at 100 V for 1 hr in a 1.0% TAE (0.04M Tris-acetate, 0.002 M EDTA) agarose gel supplemented with 0.5%ethidium bromide (Sigma-Aldrich Corporation, St. Louis, Mo.). DNAfragments were visualized with UV light and fragment size estimated bycomparison with 1 Kbp DNA ladder (Invitrogen Life Technologies,Carlsbad, Calif.). The 3.4 Kbp Spe I/Not I digested subcloning vector,pBC SK(−) was gel-excised and purified according to the manufacturer'sdirections using QIAquick Gel Extraction Kit (QIAGEN Inc., Valencia,Calif.).

In step #2, 5′- & 3′-homology flanks from IPP2K position-2 wereisolated. The following oligonucleotide primers were synthesized byIntegrated DNA Technologies, Inc. (Coralville, Iowa) under conditions ofstandard desalting and diluted with water to a concentration of 0.125μg/μl:

(SEQ ID NO: 147) 5′-GCGGCCGCTAGATAGCAGATGCAGATTGCT-3′ (SEQ ID NO: 148)5′-ACTAGTATTGGCACCCAGGTGTTGGCTCA-3′ (SEQ ID NO: 149)5′-ACTAGTCATGTCGATGGTGGGGTATGGTTCAGATTCAG-3′ (SEQ ID NO: 150)5′-GTCGACGTACAATGATTTCAGGTTACGGCCTCAGGAC-3′

PCR amplification reactions were carried out using reagents provided byTaKaRa Biotechnology Inc., Seta 3-4-1, Otsu, Shiga, 520-2193, Japan andconsisted of the following: 5 μl 10× LA PCR™ Buffer II (Mg2⁺), 20 ngdouble-stranded gDNA template (maize HiII), 10 pmol forwardoligonucleotide primer, 10 pmol reverse oligonucleotide primer, 8 μldNTP mix (2.5 mM each), 33.5 μl H₂O, 0.5 μl (2.5 units) TaKaRa LA Taq™DNA polymerase, 1 drop of mineral oil. PCR reactions were performedusing a Perkin-Elmer Cetus, 48-sample DNA Thermal Cycler (Norwalk,Conn.) under the following cycle conditions: 94° C., 4 min/1 cycle; 98°C. 20 sec, 55° C. 1 min, 68° C. 1 min/30 cycles; 72° C., 5 min/1 cycle;4° C./hold. Fifteen μl of each PCR reaction was electrophoresed at 100 Vfor 1 hr in a 1.0% TAE agarose gel supplemented with 0.5% ethidiumbromide. Amplified fragments were visualized with UV light and fragmentsize estimated by comparison with 1 Kbp DNA ladder. Expectedamplification products were diagnosed by the presence of either a DNAfragments of 0.855 Kbp (5′-homology flank) or 0.845 Kbp (3′-homologyflank). These fragments were gel-excised and purified according tomanufacturer's directions using QIAquick Gel Extraction Kit (QIAGENInc., Valencia, Calif.). Purified fragments were then cloned into pCR2.1plasmid using TOPO TA Cloning® Kit (with pCR® 2.1 vector) and One Shot®TOP10 Chemically competent E. coli cells (Invitrogen Life Technologies,Carlsbad, Calif.) according to manufacturer's protocol.

Individual colonies were inoculated into a 14 ml Falcon Tube(Becton-Dickinson, Franklin Lakes, N.J.) containing 2 ml TB supplementedwith 50 μl/ml kanamycin and incubated for 16 hrs at 37° C. with shakingat 200 rpm. Following incubation, 1.5 ml cells were transferred to a 1.7ml Costar microcentrifuge tube (Fisher Scientific, Pittsburgh, Pa.) andpelleted at 16,000×g for 1 min. Supernatant was removed and plasmid DNAwas isolated as described above using NucleoSpin® Plasmid Kit (BDBiosciences/Clontech/Macherey-Nagel, Palo Alto, Calif.). Three μg ofisolated plasmid from 5′-homology flank clone plasmids was digested with10 units Spe I and Not I. Three prime-homology flank clone plasmids weredigested with 10 units Spe I and 20 units Sal I (New England Biolabs,Beverly, Mass.). All plasmid digestions were incubated for 1 hr at 37°C.

Restricted DNA was electrophoresed at 100V for 1 hr in a 1.0% TAEagarose gel supplemented with 0.5% ethidium bromide. Fragments werevisualized with UV light and fragment size estimated by comparison with1 Kbp DNA ladder. Expected plasmid clones were diagnosed by the presenceof inserted DNA fragments of 0.855 Kbp (5′-homology flank) or 0.845 Kbp(3′-homology flank) in addition to the 3.9 Kbp pCR® 2.1 vector.

Double-stranded sequencing reactions of plasmid clones were performed asdescribed by manufacturer using CEQ™ DTCS-Quick Start Kit(Beckman-Coulter, Palo Alto, Calif.). Reactions were purified usingPerforma DTR Gel Filtration Cartridges (Edge BioSystems, Gaithersburg,Md.) as described by manufacturer protocols. Sequence reactions wereanalyzed on a Beckman-Coulter CEQ™ 2000 XL DNA Analysis System andnucleotide characterization performed using Sequencher™ version 4.1.4(Gene Codes Corporation, Ann Arbor, Mich.). The sequence of the 0.855Kbp fragment corresponding to the position-2 5′-homology flank derivedfrom IPP2K is shown in FIG. 89 (SEQ ID NO:139). The sequence of the0.845 Kbp fragment corresponding to the position-2 3′-homology flankderived from IPP2K is shown in FIG. 90 (SEQ ID NO:140).

In step #3, position-1 5′-homology flanks were ligated into the baseplasmid. Restricted fragments corresponding to clones that contained thecorrect position-2, 5′-homology flank sequence were gel-excised andpurified according to the manufacturer's directions using QIAquick GelExtraction Kit (QIAGEN Inc., Valencia, Calif.). Fragments correspondingto the position-1 5′-homology flank (0.855 Kbp) were then ligated topurified base plasmid digested with Spe I/Not I (step #1) at a 1:5vector:insert ratio using 500 units T4 DNA Ligase (Invitrogen LifeTechnologies, Carlsbad, Calif.) in a reaction volume of 20 μl underconditions of 16 hr incubation in a 16° C. water bath.

Five μl of the ligation reaction was subsequently transformed E. coliOne Shot® Top 10 Chemically Competent Cells, (Invitrogen LifeTechnologies, Carlsbad, Calif.) and plated under selection conditionsdescribed by the manufacturer. Individual colonies were inoculated intoa 14 ml Falcon Tube (Becton-Dickinson, Franklin Lakes, N.J.) containing2 ml TB supplemented with 50 μl/ml kanamycin and incubated for 16 hrs at37° C. shaking 200 rpm. Following incubation, 1.5 ml cells weretransferred to a 1.7 ml Costar microcentrifuge tube (Fisher Scientific,Pittsburgh, Pa.) and pelleted at 16,000×g for 1 min. Supernatant wasremoved and plasmid DNA was isolated as described above usingNucleoSpin® Plasmid Kit (BD Biosciences/Clontech/Macherey-Nagel, PaloAlto, Calif.). Three μg of isolated plasmid DNA was digested with 10units Spe I and Not I. (New England Biolabs, Beverly, Mass.) andincubated for 1 hr at 37° C. Restricted DNA was electrophoresed at 100 Vfor 1 hr in a 1.0% TAE agarose gel supplemented with 0.5% ethidiumbromide. Fragments were visualized with UV light and fragment sizeestimated by comparison with 1 Kbp DNA ladder. Expected plasmid cloneswere diagnosed by the presence of an inserted DNA fragment of 0.855 Kbp(5′-homology flank) in addition to the 3.4 Kbp base plasmid.

In step #4, position-2 3′-homology flanks were ligated into the step #3product. Three μg of the engineering product described in step #3 waslinearized using 10 units of Spe I and 20 units of Sal I (New EnglandBiolabs, Beverly, Mass.) restriction endonucleases for 1 hr at 37° C.Restricted DNA was electrophoresed at 100 V for 1 hr in a 1.0% TAE (0.04M Tris-acetate, 0.002 M EDTA) agarose gel supplemented with 0.5%ethidium bromide (Sigma-Aldrich Corporation, St. Louis, Mo.). DNAfragments were visualized with UV light and fragment size estimated bycomparison with 1 Kbp DNA ladder (Invitrogen Life Technologies,Carlsbad, Calif.). The 4.25 Kbp Spe I/Sal I digested product from step#3 was gel-excised and purified according to the manufacturer'sdirections using QIAquick Gel Extraction Kit (QIAGEN Inc., Valencia,Calif.).

Isolated fragments of the 3′-homology flank donor (0.845 Kbp) generatedin step #2 were subsequently combined with step #3 product that wasdigested with Spe I/Sal I and purified as described above in a 20 μlligation reaction using a 1:5 vector:insert ratio and 500 units T4 DNALigase (Invitrogen Life Technologies, Carlsbad, Calif.). Ligationreactions were incubated for 16 hr in a 16° C. water bath. Following theligation, 5 μl of the ligation reaction was transformed into MAXEfficiency® DH5α™ Chemically Competent Cells (Invitrogen LifeTechnologies, Carlsbad, Calif.) as per the manufacturer'srecommendations. Individual colonies were inoculated into a 14 ml FalconTube (Becton-Dickinson, Franklin Lakes, N.J.) containing 2 ml TBsupplemented with 50 μl/ml chloramphenicol. Cultures were incubated for16 hrs at 37° C. shaking 200 rpm. Following incubation, 1.5 ml cellswere transferred to a 1.7 ml Costar microcentrifuge tube (FisherScientific, Pittsburgh, Pa.) and pelleted at 16,000×g for 1 min.Supernatant was removed and plasmid DNA was isolated as described aboveusing NucleoSpin® Plasmid Kit (BD Biosciences/Clontech/Macherey-Nagel,Palo Alto, Calif.). Three μg isolated plasmid was digested with 10 unitsSal I and Not I (New England Biolabs, Beverly, Mass.) and incubated for1 hr at 37° C. Restricted DNA was electrophoresed at 100 V for 1 hr in a1.0% TAE agarose gel supplemented with 0.5% ethidium bromide. Fragmentswere visualized with UV light and fragment size estimated by comparisonwith 1 Kbp DNA ladder. Expected clones were diagnosed by the presence oftwo DNA fragments of ˜1.7 Kbp (insert) and 3.33 Kbp (base plasmid). Theresulting plasmid was given the name pDAB7451 (FIG. 71).

D. Autonomous Herbicide-Tolerance Gene Expression Cassette Construction

An autonomous herbicide-tolerance gene expression cassette comprising acomplete promoter-transcriptional unit (PTU) containing promoter,herbicide tolerance gene, and poly adenylation (polyA) terminationsequences was constructed (FIG. 72). In this embodiment, the promotersequence is derived from O. sativa actin 1 [McElroy et al. (Plant Cell2, 163-171; 1990); GenBank Accession S44221 and GenBank AccessionX63830]. The herbicide-tolerance gene comprises the PAT(phosphinothricin acetyl transferase) gene, which confers resistance tothe herbicide bialaphos (a modified version of the PAT coding regionoriginally derived from Streptomyces viridochromogenes (GenBankAccession M22827; Wohlleben et al. Gene 70, 25-37; 1988). Themodifications to the original sequence of the longest open reading frameof M22827 are substantial, and include altering the codon utilizationpattern to optimize expression in plants. Except for the substitution ofmethionine for valine as the first encoded amino acid, and the additionof alanine as the second encoded amino acid, the protein encoded fromthe PAT open reading frame of pDAB3014 is identical to that encoded bythe longest open reading frame of accession M22827. The rebuilt versionof PAT is found under GenBank accession I43995. The terminator sequencesare derived from Z. mays L. lipase [maize lipase cDNA clone of GenBankAccession Number L35913, except that a C at position 1093 of L35913 isreplaced with a G at position 2468 in pDAB3014. This maize sequencecomprises the 3′ untranslated region/transcription terminator region forthe PAT gene].

The following oligonucleotide primers were synthesized by Integrated DNATechnologies, Inc. (Coralville, Iowa) under conditions of standarddesalting and diluted with water to a concentration of 0.125 μg/μl:

(SEQ ID NO: 151) 5′- ACTAGTTAACTGACCTCACTCGAGGTCATTCATATGCTTGA -3′ (SEQID NO: 152) 5′- ACTAGTGTGAATTCAGCACTTAAAGATCT -3′

PCR amplification reactions were carried out using reagents provided byTaKaRa Biotechnology Inc., Seta 3-4-1, Otsu, Shiga, 520-2193, Japan andconsisted of the following: 5 μl 10× LA PCR™ Buffer II (Mg2⁺), 20 ngdouble-stranded template [pDAB3014 plasmid DNA], 10 pmol forwardoligonucleotide primer, 10 pmol reverse oligonucleotide primer, 8 μldNTP mix (2.5 mM each), 33.5 μl H₂O, 0.5 μl (2.5 units) TaKaRa LA Taq™DNA polymerase, 1 drop of mineral oil. PCR reactions were performedusing a Perkin-Elmer Cetus, 48-sample DNA Thermal Cycler (Norwalk,Conn.) under the following cycle conditions: 94° C., 4 min/1 cycle; 98°C. 20 sec, 55° C. 1 min, 68° C. 3 min/30 cycles; 72° C., 5 min/1 cycle;4° C./hold. Fifteen μl of each PCR reaction was electrophoresed at 100 Vfor 1 hr in a 1.0% TAE agarose gel supplemented with 0.5% ethidiumbromide.

Amplified fragments were visualized with UV light and fragment sizeestimated by comparison with 1 Kbp DNA ladder. Expected amplificationproducts were diagnosed by the presence of a DNA fragment of 2.3 Kbp.This fragment was gel-excised and purified according to manufacturer'sdirections using QIAquick Gel Extraction Kit (QIAGEN Inc., Valencia,Calif.). Purified fragment was then cloned into pCR2.1 plasmid usingTOPO TA Cloning® Kit and transformed into One Shot® TOP10 Chemicallycompetent E. coli cells (Invitrogen Life Technologies, Carlsbad, Calif.)according to manufacturer's protocol.

Individual colonies were inoculated into a 14 ml Falcon Tube(Becton-Dickinson, Franklin Lakes, N.J.) containing 2 ml TB supplementedwith 50 μl/ml kanamycin and incubated for 16 hrs at 37° C. with shakingat 200 rpm. Following incubation, 1.5 ml cells were transferred to a 1.7ml Costar microcentrifuge tube (Fisher Scientific, Pittsburgh, Pa.) andpelleted at 16,000×g for 1 min. Supernatant was removed and plasmid DNAwas isolated as described above using NucleoSpin® Plasmid Kit (BDBiosciences/Clontech/Macherey-Nagel, Palo Alto, Calif.). Three μg ofisolated plasmid was digested with 10 units Spe I and Not I. All plasmiddigestions were incubated for 1 hr at 37° C.

Restricted DNA was electrophoresed at 100 V for 1 hr in a 1.0% TAEagarose gel supplemented with 0.5% ethidium bromide. Fragments werevisualized with UV light and fragment size estimated by comparison with1 Kbp DNA ladder. Expected plasmid clones were diagnosed by the presenceof an inserted DNA fragment of 2.325 Kbp in addition to the 3.9 Kbp pCR®2.1 vector. Double-stranded sequencing reactions of plasmid clones wereperformed as described by manufacturer using CEQT DTCS-Quick Start Kit(Beckman-Coulter, Palo Alto, Calif.). Reactions were purified usingPerforma DTR Gel Filtration Cartridges (Edge BioSystems, Gaithersburg,Md.) as described by manufacturer protocols. Sequence reactions wereanalyzed on a Beckman-Coulter CEQ™ 200 XL DNA Analysis System andnucleotide characterization was performed using Sequencher version 4.1.4(Gene Codes Corporation, Ann Arbor, Mich.).

E. Autonomous Herbicide Tolerance Gene Cassette Insertion into PlasmidBackbone—Autonomous Donor

In order to create a donor plasmid, the autonomous herbicide tolerancegene cassette described in Example 18D was inserted into plasmidbackbone constructions described in Examples 18B and 18C. Restrictedfragment derived from a clone that contained the expected 2.325 Kbpsequence described above (FIG. 72) was gel-excised and purifiedaccording to the manufacturer's directions using QIAquick Gel ExtractionKit (QIAGEN Inc., Valencia, Calif.).

This fragment was then combined in a ligation reaction with eitherpurified pDAB7471 (position-1 plasmid backbone, FIG. 70) or pDAB 7451(position-2 plasmid backbone FIG. 71) that had been digested withrestriction enzyme Spe I and subsequently dephosphorylated. Ligation wascarried out under the following conditions: 1:5 vector:insert ratio and500 units T4 DNA Ligase (Invitrogen Life Technologies, Carlsbad, Calif.)in a reaction volume of 20 μl under conditions of 16 hr incubation in a16° C. water bath. Five μl of the ligation reaction was subsequentlytransformed into 50 μl E. coli MAX Efficiency® DH5α™ ChemicallyCompetent Cells, (Invitrogen Life Technologies, Carlsbad, Calif.) andplated under selection conditions described by the manufacturer.

Individual colonies were inoculated into a 14 ml Falcon Tube(Becton-Dickinson, Franklin Lakes, N.J.) containing 2 ml TB supplementedwith 50 μl/ml chloramphenicol and incubated for 16 hrs at 37° C. shaking200 rpm. Following incubation, 1.5 ml cells were transferred to a 1.7 mlCostar microcentrifuge tube (Fisher Scientific, Pittsburgh, Pa.) andpelleted at 16,000×g for 1 min. Supernatant was removed and plasmid DNAwas isolated as described above using NucleoSpin® Plasmid Kit (BDBiosciences/Clontech/Macherey-Nagel, Palo Alto, Calif.). Three μg ofisolated plasmid DNA was digested with 10 units Spe I (New EnglandBiolabs, Beverly, Mass.) and incubated for 1 hr at 37° C. Restricted DNAwas electrophoresed at 100 V for 1 hr in a 1.0% TAE agarose gelsupplemented with 0.5% ethidium bromide. Fragments were visualized withUV light and fragment size estimated by comparison with 1 Kbp DNAladder. Expected plasmid clones were diagnosed by the presence of DNAfragments of 2.325 Kbp and ˜4.9 Kbp (pDAB7471 vector) or 2.325 Kbp and˜5.0 Kbp (pDAB7451 vector).

The resulting plasmids were named pDAB7422 (position-1 autonomous donor)(FIG. 73) and pDAB7452 (position-2 autonomous donor) (FIG. 74),respectively.

F. Non-Autonomous Herbicide-Tolerance Gene Expression CassetteConstruction

A non-autonomous herbicide-tolerance gene expression cassette comprisingan incomplete promoter-transcriptional unit (PTU) was constructed (FIG.75). In this embodiment, a strategy was used that exploits thefunctionality of a 2A sequence (Mattion, N. M., Harnish, E. C., Crowley,J. C. & Reilly, P. A. (1996) J. Virol. 70, 8124-8127) derived from theThesoa assigna virus, a herbicide tolerance gene and poly adenylation(polyA) termination sequences, but no promoter. In this embodiment, the2A translational termination signal sequence has been engineered to betranslationally in-frame with the herbicide tolerance gene. In addition,the 2A/herbicide coding sequence has been engineered to coincide withthe translational reading frame of the IPP2K gene target. Theherbicide-tolerance gene comprises the PAT (phosphinothricin acetyltransferase) gene, which confers resistance to the herbicide bialaphos(a modified version of the PAT coding region originally derived fromStreptomyces viridochromogenes (GenBank Accession M22827; Wohlleben etal. Gene 70:25-37; 1988). The modifications to the original sequence ofthe longest open reading frame of M22827are substantial, and includealtering the codon utilization pattern to optimize expression in plants.Except for the substitution of methionine for valine as the firstencoded amino acid, and the addition of alanine as the second aminoacid, the protein encoded from the PAT open reading frame of pDAB3014 isidentical to that encoded by the longest open reading frame of M22827(which starts with GTG at position 244 of M22827). The rebuilt versionof PAT is found under GenBank accession I43995. The terminator sequencesare derived from Z. mays L. lipase [maize lipase cDNA clone of GenBankAccession Number L35913, except that a C at position 1093 of L35913 isreplaced with a G at position 2468 in pDAB3014]. This maize sequencecomprises the 3′ untranslated region/transcription terminator region forthe PAT gene.

The following oligonucleotide primers were synthesized by Integrated DNATechnologies, Inc. (Coralville, Iowa) under conditions of standarddesalting and diluted with water to a concentration of 0.125 μg/μl:

(SEQ ID NO: 153) 5′- ACTAGTGGCGGCGGAGAGGGCAGAGGAAGTCTTCTAACATGCGGTGACGTGGAGGAGAATCCCGGCCCTAGGATGGCTTCTCCGGAGAGGAG ACCAGTTGA -3 (SEQ IDNO: 154) 5′- ACTAGTATGCATGTGAATTCAGCACTTAAAGATCT -3′

PCR amplification reactions were carried out using reagents provided byTaKaRa Biotechnology Inc. (Seta 3-4-1, Otsu, Shiga, 520-2193, Japan) andconsisted of the following: 5 μl 10× LA PCR™ Buffer II (Mg2⁺), 20 ngdouble-stranded template (pDAB3014 plasmid DNA), 10 pmol forwardoligonucleotide primer, 10 pmol reverse oligonucleotide primer, 8 μldNTP mix (2.5 mM each), 33.5 μl H₂O, 0.5 μl (2.5 units) TaKaRa LA Taq™DNA polymerase, 1 drop of mineral oil. PCR reactions were performedusing a Perkin-Elmer Cetus, 48-sample DNA Thermal Cycler (Norwalk,Conn.) under the following cycle conditions: 94° C., 4 min/1 cycle; 98°C. 20 sec, 55° C. 1 min, 68° C. 2 min/30 cycles; 72° C., 5 min/1 cycle;4° C./hold. Fifteen μl of each PCR reaction was electrophoresed at 100 Vfor 1 hr in a 1.0% TAE agarose gel supplemented with 0.5% ethidiumbromide. Amplified fragments were visualized with UV light and fragmentsize estimated by comparison with 1 Kbp DNA ladder. Expectedamplification products were diagnosed by the presence of a DNA fragmentof 1 Kbp. This fragment was gel-excised and purified according tomanufacturer's directions using QIAquick Gel Extraction Kit (QIAGENInc., Valencia, Calif.). Purified fragment were then cloned into pCR2.1plasmid using TOPO TA Cloning® Kit transformed into One Shot® TOP10chemically competent E. coli cells (Invitrogen Life Technologies,Carlsbad, Calif.) according to manufacturer's protocol.

Individual colonies were inoculated into a 14 ml Falcon Tube(Becton-Dickinson, Franklin Lakes, N.J.) containing 2 ml TB supplementedwith 50 μl/ml kanamycin and incubated for 16 hrs at 37° C. with shakingat 200 rpm. Following incubation, 1.5 ml cells were transferred to a 1.7ml Costar microcentrifuge tube (Fisher Scientific, Pittsburgh, Pa.) andpelleted at 16,000×g for 1 min. Supernatant was removed and plasmid DNAwas isolated as described above using NucleoSpin® Plasmid Kit (BDBiosciences/Clontech/Macherey-Nagel, Palo Alto, Calif.). Three μg ofisolated plasmid was digested with 10 units Spe I. All plasmiddigestions were incubated for 1 hr at 37° C. Restricted DNA waselectrophoresed at 100 V for 1 hr in a 1.0% TAE agarose gel supplementedwith 0.5% ethidium bromide. Fragments were visualized with UV light andfragment size estimated by comparison with 1 Kbp DNA ladder. Expectedplasmid clones were diagnosed by the presence of an inserted DNAfragment of 1.0 Kbp and 3.9 Kbp (pCR® 2.1 vector). Double-strandedsequencing reactions of plasmid clones were performed as described bymanufacturer using CEQ™ DTCS-Quick Start Kit (Beckman-Coulter, PaloAlto, Calif.). Reactions were purified using Performa DTR Gel FiltrationCartridges (Edge BioSystems, Gaithersburg, Md.) as described bymanufacturer protocols. Sequence reactions were analyzed on aBeckman-Coulter CEQ™ 2000 XL DNA Analysis System and nucleotidecharacterization performed using Sequencher™ version 4.1.4 (Gene CodesCorporation, Ann Arbor, Mich.).

G. Non-Autonomous Herbicide Tolerance Gene Cassette Insertion intoPlasmid Backbone—Non-Autonomous Donor

In order to create a donor plasmid, the non-autonomousherbicide-tolerance gene cassette described in Example 18F was insertedinto the plasmid backbone constructions described in Examples 18B and18C. Restricted fragment corresponding to a clone that contained thecorrect 1 Kbp sequence was gel-excised and purified according to themanufacturer's directions using QIAquick Gel Extraction Kit (QIAGENInc., Valencia, Calif.). This fragment was then combined in a ligationreaction with either purified pDAB7471 (position-1 plasmid backbone)(FIG. 70) or pDAB 7451 (position-2 plasmid backbone) (FIG. 71) that hadbeen digested with restriction enzyme Spe I and subsequentlydephosphorylated. Ligation was carried out under the followingconditions: 1:5 vector:insert ratio and 500 units T4 DNA Ligase(Invitrogen Life Technologies, Carlsbad, Calif.) in a reaction volume of20 μl under conditions of 16 hr incubation in a 16° C. water bath. Fiveμl of the ligation reaction was subsequently transformed into 50 μl E.coli MAX Efficiency® DH5α™ Chemically Competent Cells, (Invitrogen LifeTechnologies, Carlsbad, Calif.) and plated under selection conditionsdescribed by the manufacturer.

Individual colonies were inoculated into a 14 ml Falcon Tube(Becton-Dickinson, Franklin Lakes, N.J.) containing 2 ml TB supplementedwith 50 μl/ml chloramphenicol and incubated for 16 hrs at 37° C. shaking200 rpm. Following incubation, 1.5 ml cells were transferred to a 1.7 mlCostar microcentrifuge tube (Fisher Scientific, Pittsburgh, Pa.) andpelleted at 16,000×g for 1 min. Supernatant was removed and plasmid DNAwas isolated as described above using NucleoSpin® Plasmid Kit (BDBiosciences/Clontech/Macherey-Nagel, Palo Alto, Calif.). Three μg ofisolated plasmid DNA was digested with 10 units Spe I (New EnglandBiolabs, Beverly, Mass.) and incubated for 1 hr at 37° C. Restricted DNAwas electrophoresed at 100 V for 1 hr in a 1.0% TAE agarose gelsupplemented with 0.5% ethidium bromide. Fragments were visualized withUV light and fragment size estimated by comparison with 1 Kbp DNAladder. Expected plasmid clones were diagnosed by the presence of DNAfragments 1.0 Kbp and 4.96 Kbp (pDAB7471 vector) or 1.0 Kbp and ˜5.0 Kbp(pDAB7451 vector). The resulting plasmids were named pDAB7423(position-1 non-autonomous donor) (FIG. 76) and pDAB7454 (position-2non-autonomous donor) (FIG. 77), respectively.

H. Position 1 ZFN+HR Donor Sequences: Combination Plasmid.

As an alternative strategy to the delivery of two separate plasmids intoa plant cell (e.g. one plasmid containing ZFN elements and a secondcontaining the herbicide tolerance donor sequences), single plasmidswere engineered containing all necessary elements illustrated in thispatent. The combination plasmids described in this example contains boththe ZFNs designed to target and generate double-strand breaks at thespecified IPP2K locus as well as the autonomous PAT PTU and/ornon-autonomous 2A/PAT PTU and donor flanks designed to integrate intothose break sites.

Gateway® technology, which uses lambda phage-based site-specificrecombination (Landy, A. (1989) Ann. Rev. Biochem. 58:913) was utilizedto convert vectors pDAB7422 and pDAB7423 (described in examples 6E and6G) into Gateway® destination vectors. Once converted, plasmidscontaining ZFN expression cassettes (housed in Gateway® Entry vectors)can be mobilized easily to the destination vector creating a ZFN/donorcombination plasmid. One μg of each such plasmid was digested with 10units Not I (New England Biolabs, Beverly, Mass.) for 1 hr at 37° C. NotI restriction endonuclease was heat-inactivated at 65° C. for 15 min andfragment ends subsequently dephosphorylated at 37° C. for 1 hr using 3units of shrimp alkaline phosphatase (SAP) (Roche Diagnostics GmbH,Mannheim, Germany). Restricted DNA was electrophoresed at 100 V for 1 hrin a 1.0% TAE agarose gel supplemented with 0.5% ethidium bromide.Vector fragments (pDB7422=7.317 Kbp, pDAB7423=5.971 Kbp) were visualizedwith UV light, size estimated by comparison with 1 Kbp DNA ladder,gel-excised and subsequently purified according to the manufacturer'sdirections using QIAquick Gel Extraction Kit (QIAGEN Inc., Valencia,Calif.).

This vector fragment was then combined with a 2.274 Kbp Not I fragmentcontaining Gateway® Technology elements attR1, ccdB, Cm^(R), and attR2in a ligation reaction carried out under the following conditions: 1:5vector:insert ratio and 500 units T4 DNA Ligase (Invitrogen LifeTechnologies, Carlsbad, Calif.) in a reaction volume of 20 μl underconditions of 16 hr incubation in a 16° C. water bath. Five μl of theligation reaction was subsequently transformed into 50 μl E. coli OneShot® ccdB Survival™ Chemically Competent Cells, (Invitrogen LifeTechnologies, Carlsbad, Calif.) and plated under selection conditionsdescribed by the manufacturer.

Individual colonies were inoculated into a 14 ml Falcon Tube(Becton-Dickinson, Franklin Lakes, N.J.) containing 2 ml TB supplementedwith 50 μl/ml chloramphenicol and incubated for 16 hrs at 37° C. shaking200 rpm. Following incubation, 1.5 ml cells were transferred to a 1.7 mlCostar microcentrifuge tube (Fisher Scientific, Pittsburgh, Pa.) andpelleted at 16,000×g for 1 min. Supernatant was removed and plasmid DNAwas isolated as described above using NucleoSpin® Plasmid Kit (BDBiosciences/Clontech/Macherey-Nagel, Palo Alto, Calif.). Three μg ofisolated plasmid DNA was digested with 10 units EcoRI I (New EnglandBioLabs, Inc., Beverly, Mass.) and incubated for 1 hr at 37° C.Restricted DNA was electrophoresed at 100 V for 1 hr in a 1.0% TAEagarose gel supplemented with 0.5% ethidium bromide. Fragments werevisualized with UV light and fragment size estimated by comparison with1 Kbp DNA ladder. Expected plasmid clones were diagnosed by the presenceof DNA fragments of 1.448 Kbp, 1.946 Kbp, and 6.197 Kbp for theautonomous PAT PTU position-1 HR donor and 5.807 Kbp and 2.438 Kbp forthe non-autonomous PAT position-1 HR donor. The resulting plasmids werenamed pDAB7424 (Gateway® adapted position-1 autonomous donor) (FIG. 78)and pDAB7425 (Gateway® adapted position-1 non-autonomous donor) (FIG.79), respectively.

As a result of these cloning manipulations, the plasmids pDAB7424 &pDAB7425 were designated as Gateway® destination vectors. pDAB7412 hasfunctionality as a Gateway® entry vector containing the followingelements: ZmUbi1v.2/ZFN12/Zm Per5 3′ UTR. To transfer a ZFN expressioncassette (Gateway® entry vector) into either autonomous ornon-autonomous donor molecule (Gateway® destination vector), a LRClonase™ II (Invitrogen Life Technologies, Carlsbad, Calif.) reactionwas performed as outlined by the manufacturer at a ratio of 50 ng (Entryvector): 150 ng/μl (Destination vector). The resulting positivecombination plasmids were named pDAB7426 (position-1 autonomous HRdonor/ZFN12) (FIG. 80) & pDAB7427 (non-autonomous HR donor/ZFN12) (FIG.81).

Example 19 ZFN and Donor DNA Delivery into Plant Cells

In order to enable ZFN-mediated integration of donor DNA into the plantgenome via targeted integration, it is understood that delivery ofZFN-encoding DNA followed by expression of functional ZFN protein in theplant cell is required. Also required is concomitant delivery of donorDNA into said plant cell, such that functional ZFN protein may inducedouble-stranded breaks at the target DNA which are then repaired viahomology driven integration of the donor DNA into the target locus. Oneskilled in the art may envision that expression of functional ZFNprotein may be achieved by several methods, including, but not limitedto transgenesis of the ZFN-encoding construction, or transientexpression of the ZFN-encoding construction. In both these cases,expression of functional ZFN protein and delivery of donor DNA in theplant cell is simultaneously achieved in order to drive targetedintegration.

In the examples cited here, we demonstrate methods for the concomitantdelivery of ZFN-encoding and donor DNA into plant cells. One skilled inthe art might use any of a variety of DNA-delivery methods appropriatefor plant cells, including, but not limited to, Agrobacterium-mediatedtransformation, biolistics-based DNA delivery or Whiskers™-mediated DNAdelivery. In one embodiment described here, Whiskers™-mediated DNAdelivery experiments were carried out using various combinations ofdonor DNA with ZFN-encoding DNA constructions. These combinationsinclude 1) a single plasmid containing both ZFN-encoding sequence anddonor DNA and 2) two distinct plasmids, one containing ZFN-encodingsequence and the other containing donor DNA. In another embodiment,biolistics-based DNA-delivery was carried out using various combinationsof donor DNA with ZFN-encoding DNA constructions. One skilled in the artmay deduce that these combinations might include 1) a single plasmidcontaining both ZFN-encoding sequence and donor DNA and 2) two distinctplasmids, one containing ZFN-encoding sequence and the other containingdonor DNA.

A. Whiskers™-Mediated DNA Delivery

As described earlier herein, embryogenic Hi-II cell cultures of maizewere produced, and were used as the source of living plant cells inwhich targeted integration is demonstrated. One skilled in the art mayenvision the utilization of cell cultures derived from a variety ofplant species, or differentiated plant tissues derived from a variety ofplant species, as the source of living plant cells in which targetedintegration is demonstrated.

In this example, 12 ml PCV from a previously cryo-preserved cell lineplus 28 ml of conditioned medium was subcultured into 80 ml of GN6liquid medium (N6 medium (Chu et al., 1975), 2.0 mg/L 2, 4-D, 30 g/Lsucrose, pH 5.8) in a 500 ml Erlenmeyer flask, and placed on a shaker at125 rpm at 28° C. This step was repeated 2 times using the same cellline such that a total of 36 ml PCV was distributed across 3 flasks.After 24 hours the GN6 liquid media was removed and replaced with 72 mlGN6 S/M osmotic medium (N6 Medium, 2.0 mg/L 2,4-D, 30 g/L sucrose, 45.5g/L sorbitol, 45.5 g/L mannitol, 100 mg/L myo-inositol, pH 6.0). Theflask was incubated in the dark for 30-35 minutes at 28° C. withmoderate agitation (125 rpm). During the incubation period, a 50 mg/mlsuspension of silicon carbide whiskers (Advanced Composite Materials,LLC, Greer, S.C.) was prepared by adding 8.1 ml of GN6 S/M liquid mediumto 405 mg of sterile, silicon carbide whiskers.

Following incubation in GN6 S/M osmotic medium, the contents of eachflask were pooled into a 250 ml centrifuge bottle. After all cells inthe flask settled to the bottom, contents volume in excess ofapproximately 14 ml of GN6 S/M liquid was drawn off and collected in asterile 1-L flask for future use. The pre-wetted suspension of whiskerswas mixed at maximum speed on a vortex for 60 seconds, and then added tothe centrifuge bottle.

In one example, wherein a single plasmid containing both theZFN-encoding sequence plus the donor DNA is being delivered into theplant cells, 170 μg of purified circular plasmid DNA was added to thebottle. In an alternative example, wherein two distinct plasmids werebeing co-delivered, one containing ZFN-encoding sequence and the othercontaining donor DNA, multiple strategies for DNA amounts were assessed.One strategy utilized 85 μg of donor DNA and 85 μg of zinc-fingerencoding DNA. Other modifications utilized molar ratios of 10, 5, or1-fold donor DNA to 1-fold zinc finger DNA, based on the size (inkilobase pairs) of the individual plasmids such that a total of 170 μgof DNA was added per bottle. In all cases of co-delivery, DNA waspre-pooled in a tube prior to being added to the centrifuge bottle. OnceDNA was added, the bottle was immediately placed in a modified Red Devil5400 commercial paint mixer (Red Devil Equipment Co., Plymouth, Minn.)and agitated for 10 seconds. Following agitation, the cocktail of cells,media, whiskers and DNA was added to the contents of a 1-L flask alongwith 125 ml fresh GN6 liquid medium to reduce the osmoticant. The cellswere allowed to recover on a shaker set at 125 rpm for 2 hours. Six mLof dispersed suspension was filtered onto Whatman #4 filter paper (5.5cm) using a glass cell collector unit connected to a house vacuum linesuch that 60 filters were obtained per bottle. Filters were placed onto60×20 mm plates of GN6 solid medium (same as GN6 liquid medium exceptwith 2.5 g/L Gelrite gelling agent) and cultured at 28° C. under darkconditions for 1 week.

B: Biolistics-Mediated DNA Delivery

In the examples cited here, embryogenic suspensions of maize weresubcultured into GN6 liquid medium approximately 24 hours prior toexperimentation as described earlier herein. The excess liquid mediumwas removed and approximately 0.4 PCV of cells were thinly spread in acircle 2.5 cm in diameter over the center of a 100 ×15 mm petri dishcontaining GN6 S/M media solidified with 2.5 g/L gelrite. The cells werecultured under dark conditions for 4 hours. To coat the biolisticparticles with DNA, 3 mg of 1.0 micron diameter gold particles werewashed once with 100% ethanol, twice with sterile distilled water andresuspended in 50 μl water in a siliconized Eppendorf tube. A total of 5μg of plasmid DNA, 20 μl spermidine (0.1 M) and 50 μl calcium chloride(2.5 M) were added separately to the gold suspension and mixed on avortex. The mixture was incubated at room temperature for 10 min,pelleted at 10,000 rpm in a benchtop microcentrifuge for 10 seconds,resuspended in 60 μl cold 100% ethanol, and 8-9 μl was distributed ontoeach macrocarrier.

Bombardment took place using the Biolistic PDS-1000/He™ system (Bio-RadLaboratories, Hercules, Calif.). Plates containing the cells were placedon the middle shelf under conditions of 1100 psi and 27 inches of Hgvacuum, and were bombarded following the operational manual. Sixteenhours post-bombardment, the tissue was transferred in small clumps toGN6 (1H) medium and cultured for 2-3 weeks at 28° C. under darkconditions. Transfers continued every 2-4 weeks until putativetransgenic isolates resulting from integration of donor DNA appeared.Identification, isolation and regeneration of putative donor DNAintegration events generated via biolistic-mediated DNA delivery isidentical to the process utilized for putative donor DNA integrationevents generated via Whiskers™-mediated DNA delivery and describedbelow.

C. Identification and Isolation of Putative Targeted IntegrationTransgenic Events

One week post-DNA delivery, filter papers were transferred to 60×20 mmplates of GN6 (1H) selection medium (N6 Medium, 2.0 mg/L 2,4-D, 30 g/Lsucrose, 100 mg/L myo-inositol, 1.0 mg/L bialaphos from Herbiace (MeijiSeika, Japan), 2.5 g/L Gelrite, pH 5.8). These selection plates wereincubated at 28° C. for one week in the dark.

Following 1 week of selection in the dark, the tissue was embedded ontofresh media by scraping half the cells from each plate into a tubecontaining 3.0 mL of GN6 agarose medium held at 37-38° C. (N6 medium,2.0 mg/L 2,4-D, 30 g/L sucrose, 100 mg/L myo-inositol, 7 g/L SeaPlaque®agarose, pH 5.8, autoclaved for only 10 minutes at 12° C.) and 1 mg/Lbialaphos from Herbiace.

The agarose/tissue mixture was broken up with a spatula, andsubsequently 3 mL of agarose/tissue mixture was evenly poured onto thesurface of a 100×15 mm petri dish containing GN6 (1H) medium. Thisprocess was repeated for both halves of each plate. Once all the tissuewas embedded, plates were individually sealed with Nescofilm® orParafilm M®, and cultured at 28° C. under dark conditions for up to 10weeks. Putatively transformed isolates that grew under these selectionconditions were removed from the embedded plates and transferred tofresh selection medium in 60×20 mm plates. If sustained growth wasevident after approximately 2 weeks, an event was deemed to be resistantto the applied herbicide (bialophos) and an aliquot of cells wassubsequently harvested into 2 mL Eppendorf tubes for genotype analysis.

One skilled in the art might utilize a gene encoding any appropriateselectable marker in the donor DNA and apply comparable selectionconditions to living cells. For example, an alternative selectablemarker gene such as AAD-1, as described in WO 2005/107437 A2, could beimplemented as a donor for selection and recovery of integrated eventsin maize cells as described herein.

Example 20 Screening for Targeted Integration Events Via PCR Genotyping

In this example, PCR genotyping is understood to include, but not belimited to, polymerase-chain reaction (PCR) amplification of genomic DNAderived from isolated maize callus tissue predicted to contain donor DNAembedded in the genome, followed by standard cloning and sequenceanalysis of PCR amplification products. Methods of PCR genotyping havebeen well described (for example, Rios, G. et al. (2002) Plant J.32:243-253) and may be applied to genomic DNA derived from any plantspecies or tissue type, including cell cultures.

One skilled in the art may devise strategies for PCR-genotyping thatinclude (but are not limited to) amplification of specific sequences inthe plant genome, amplification of multiple specific sequences in theplant genome, amplification of non-specific sequences in the plantgenome, or combinations thereof. Amplification may be followed bycloning and sequencing, as described in this example, or by directsequence analysis of amplification products. One skilled in the artmight envision alternative methods for analysis of the amplificationproducts generated herein.

In one embodiment described herein, oligonucleotide primers specific forthe gene target are employed in PCR amplifications. In anotherembodiment described herein, oligonucleotide primers specific for donorDNA sequences are employed in PCR amplifications. Another embodimentincludes a combination of oligonucleotide primers that bind to both genetarget sequence and donor DNA sequence. One skilled in the art maydevise additional combinations of primers and amplification reactions tointerrogate the genome.

A. Genomic DNA Extraction

Genomic DNA (gDNA) was extracted from isolated, herbicide-tolerant,maize cells described in Example 19 and utilized as template for PCRgenotyping experiments. gDNA was extracted from approximately 100-300 μlpacked cell volume (PCV) of herbicide-tolerant HiII callus that wereisolated as described above according to the manufacturer's protocolsdetailed in the DNeasy® 96 Plant Kit (QIAGEN Inc., Valencia, Calif.).Genomic DNA was eluted in 100 μl of kit-supplied elution buffer yieldingfinal concentrations of 20-200 ng/μl and subsequently analyzed viaPCR-based genotyping methods outlined below.

B. Primer Design for PCR Genotyping

One skilled in the art might use a variety of strategies for the designand implementation of PCR-based genotypying. Oligonucleotide primersdesigned to anneal to the gene target, donor DNA sequences and/orcombinations of the two are feasible. In order to design oligonucleotideprimers that can anneal to the IPP2K gene target in regions notencompassed by the homology flanks constructed into the donor DNAmolecules, plasmid clones containing additional gene target sequencedata were characterized via DNA sequencing. Double-stranded sequencingreactions of plasmid clones were performed as described by manufacturerusing CEQT DTCS-Quick Start Kit (Beckman-Coulter, Palo Alto, Calif.).Reactions were purified using Performa DTR Gel Filtration Cartridges(Edge BioSystems, Gaithersburg, Md.) as described by manufacturerprotocols. Sequence reactions were analyzed on a Beckman-Coulter CEQ™2000 XL DNA Analysis System and nucleotide characterization performedusing Sequencher version 4.1.4 (Gene Codes Corporation, Ann Arbor,Mich.). These sequences correspond to regions of the IPP2K gene upstream(5′-) and downstream (3′-) of the ZFN targeted regions and are describedin FIG. 91 (SEQ ID NO:141) and FIG. 92 (SEQ ID NO: 142).

In the examples presented here, all oligonucleotide primers weresynthesized by Integrated DNA Technologies, Inc. (Coralville, Iowa)under conditions of standard desalting and diluted with water to aconcentration of 100 μM. The following set of forward and reverseoligonucleotide primers were designed to anneal to gDNA sequencesspecific for the IPP2K gene target that lie outside the boundaries ofthe donor DNA sequences. These oligonucleotides are as follows:

(SEQ ID NO: 153) 5′-TGGACGGAGCGAGAGCCAGAATTCGACGCT G-3′ (SEQ ID NO: 154)5′-GTGCAAGAATGTATTGGGAATCAACCTGAT G-3′

A second set of forward and reverse oligonucleotide primers were alsodesigned to anneal to gDNA sequence specific for the IPP2K gene targetoutside the boundaries of the donor DNA sequences, yet nested within thefirst pair:

(SEQ D NO: 155) 5′-CTGTGGTACCAGTACTAGTACCAGCATC-3′ (SEQ ID NO: 156)5′-TCT TGGATCAAGGCATCAAGC ATTCCAATCT-3′

Forward and reverse oligonucleotide primers were additionally designedto anneal specifically to donor DNA corresponding to coding region ofthe herbicide-tolerance gene:

5′-TGGGTAACTGGCCTAACTGG-3′ (SEQ ID NO: 157) 5′-TGGAAGGCTAGGAACGCTTA-3′(SEQ ID NO: 158) 5′-CCAGTTAGGCCAGTTACCCA-3′ (SEQ ID NO: 159)5′ TAAGCGTTCCTAGCCTTCCA-3′ (SEQ ID NO: 160)

C. Donor DNA—Specific PCR Amplification

Primary PCR amplification reactions were carried out using reagentsprovided by TaKaRa Biotechnology Inc., Seta 3-4-1, Otsu, Shiga,520-2193, Japan and consisted of the following: 2.5 μl 10× Ex Taq PCR™Buffer, 40-200 ng double-stranded genomic DNA template, 10 μM forwardoligonucleotide primer, 10 μM reverse oligonucleotide primer, 2 μl dNTPmix (2.5 mM each), 16 μl H₂O, 0.5 μl (2.5 units) Ex Taq™ DNA polymerase.PCR reactions were performed using a Bio-Rad, 96-sample DNA EngineTetrad2, Peltier Thermal Cycler (Hercules, Calif.) under the followingcycle conditions: 94° C., 3 min/1 cycle; 94° C. 30 sec, 64° C. 30 sec,72° C. 5 min/35 cycles; 72° C, 10 min/1 cycle; 4° C./hold.

Amplification products of the primary PCR reaction were subsequentlyre-amplified in a secondary PCR reaction comprised of the following: 2.5μl 10× Ex Taq PCR™ Buffer, 2 μl template (1:100 dilution of 1° PCRreaction in H₂O), 10 μM forward oligonucleotide primer, 10 μM reverseoligonucleotide primer, 2 μl dNTP mix (2.5 mM each), 16 μl H₂O, 0.5 μl(2.5 units) Ex Taq™ DNA polymerase. PCR reactions were performed using aBio-Rad, 96-sample DNA Engine Tetrad2, Peltier Thermal Cycler (Hercules,Calif.) under the following cycle conditions: 95° C., 1 min/1 cycle; 94°C. 15 sec, 61° C. 30 sec, 72° C. 30 sec/30 cycles; 72° C., 1 min/1cycle; 4° C./hold. Ten μl of each amplified product was electrophoresedat 100 V for 1 hr in a 1.0% TAE agarose gel supplemented with 0.5%ethidium bromide. Amplified fragments were visualized with UV light andfragment size estimated by comparison with 1 Kbp Plus DNA ladder(Invitrogen Life Technologies, Carlsbad, Calif.). PCR productscontaining the expected fragment were diagnosed by the presence of a DNAfragment 0.317 Kbp, as shown in FIG. 82.

Example 21 Detection of Targeted Integration Events

Of the herbicide-tolerant events containing an integrated donor DNAmolecule encoding an herbicide-tolerance gene cassette, it is expectedthat some proportion of said events are the product of targetedintegration of donor DNA into the site of the ZFN-induceddouble-stranded break. In order to differentiate these targetedintegration events from those derived from random integration of theherbicide-tolerance gene cassette, a PCR-based genotyping strategy usinga combination of genome-specific and subsequent genome-specific plusdonor-specific PCR primers was utilized.

A. Genome-Specific and Subsequent Genome/Donor Specific Amplification

In this embodiment, primary PCR reactions utilized oligonucleotideprimers specific for the regions of the IPP2K gene target upstream anddownstream of the donor integration region (e.g., FIGS. 92 and 93).Primary PCR amplification reactions were carried out using reagentsprovided by TaKaRa Biotechnology Inc., Seta 3-4-1, Otsu, Shiga,520-2193, Japan and consisted of the following: 2.5 μl 10× Ex Taq PCR™Buffer, 40-200 ng double-stranded maize gDNA template, 10 μM forwardoligonucleotide primer, 10 μM reverse oligonucleotide primer, 2 μl dNTPmix (2.5 mM each), 16 μl H₂O, 0.5 μl (2.5 units) Ex Taq™ DNA polymerase.PCR reactions were performed using a Bio-Rad, 96-sample DNA EngineTetrad2, Peltier Thermal Cycler (Hercules, Calif.) under the followingcycle conditions: 94° C., 3 min/1 cycle; 94° C. 30 sec, 64° C 30 sec,72° C. 5 min/35 cycles; 72° C., 10 min/1 cycle; 4° C./hold.

The primary PCR reaction product was subsequently diluted 1:100 in H₂Oand used as template DNA for two distinct secondary PCR reactions. Inthis embodiment, the secondary reactions utilize primers that bind inthe IPP2K genomic region and the donor molecule, giving rise to anamplicon that spans the boundary of integration between genome anddonor. The first reaction focused on the 5′-boundary between genome anddonor. The second reaction focused on the 3′-boundary between donor andgenome. Both reactions consisted of the following: 2.5 μl 10× Ex TaqPCR™ Buffer, 2 μl template [1:100 dilution of 1° PCR reaction], 10 μMforward oligonucleotide primer, 10 μM reverse oligonucleotide primer, 2μl dNTP mix (2.5 mM each), 16 μl H₂O, 0.5 μl (2.5 units) Ex Taq™ DNApolymerase. PCR reactions were performed using a Bio-Rad, 96-sample DNAEngine Tetrad2, Peltier Thermal Cycler (Hercules, Calif.) under thefollowing cycle conditions: 94° C., 3 min/1 cycle; 94° C. 30 sec, 60° C.30 sec, 72° C. 2 min/35 cycles; 72° C., 10 min/1 cycle; 4° C./hold.Twenty μL of each 2° PCR reaction was electrophoresed at 100 V for 1 hrin a 1.0% TAE agarose gel supplemented with 0.5% ethidium bromide.

Amplified fragments were visualized with UV light and fragment sizeestimated by comparison with 1 Kbp Plus DNA ladder (Invitrogen LifeTechnologies, Carlsbad, Calif.). PCR products derived from targetedintegration of donor into the IPP2K gene were diagnosed by the presenceof DNA fragments 1.65 Kbp (5′-boundary) (FIG. 83) or 1.99 Kbp(3′-boundary) (FIG. 84). These fragments were gel-excised and purifiedaccording to manufacturer's directions using QIAquick Gel Extraction Kit(QIAGEN Inc., Valencia, Calif.). Purified fragments were subsequentlycloned into pCR2.1 plasmid using TOPO TA Cloning® Kit (with pCR® 2.1vector) and One Shot® TOP10 Chemically competent E. coli cells(Invitrogen Life Technologies, Carlsbad, Calif.) according tomanufacturer's protocol.

Individual colonies were inoculated into a 14 ml Falcon Tube(Becton-Dickinson, Franklin Lakes, N.J.) containing 2 ml TB supplementedwith 50 μl/ml kanamycin and incubated for 16 hrs at 37° C. with shakingat 200 rpm. Following incubation, 1.5 ml cells were transferred to a 1.7ml Costar microcentrifuge tube (Fisher Scientific, Pittsburgh, Pa.) andpelleted at 16,000×g for 1 min. Supernatant was removed and plasmid DNAwas isolated as described above using NucleoSpin® Plasmid Kit (BDBiosciences/Clontech/Macherey-Nagel, Palo Alto, Calif.). Three μg ofisolated plasmid was digested with 10 units Eco RI (New England Biolabs,Beverly, Mass.). All plasmid digestions were incubated for 1 hr at 37°C. Restricted DNA was electrophoresed at 100 V for 1 hr in a 1.0% TAEagarose gel supplemented with 0.5% ethidium bromide. Fragments werevisualized with UV light and fragment size estimated by comparison with1 Kbp Plus DNA ladder (Invitrogen Life Technologies, Carlsbad, Calif.).

Expected plasmid clones were diagnosed by the presence of inserted DNAfragments of the appropriate size in addition to the 3.9 Kbp pCR® 2.1vector. Double-stranded sequencing reactions of plasmid clones wereperformed as described by manufacturer using CEQT DTCS-Quick Start Kit(Beckman-Coulter, Palo Alto, Calif.). Reactions were purified usingPerforma DTR Gel Filtration Cartridges (Edge BioSystems, Gaithersburg,Md.) as described by manufacturer protocols. Sequence reactions wereanalyzed on a Beckman-Coulter CEQ™ 2000 XL DNA Analysis System andnucleotide characterization performed using Sequencher™ version 4.1.4(Gene Codes Corporation, Ann Arbor, Mich.). Nucleotide alignments wereperformed using Vector NTi version 10.1 (Invitrogen Life Technologies,Carlsbad, Calif.).

Analysis of sequence data from a targeted integration event (event #073)was conducted as follows. Primary PCR products spanning the entireintegration site of the genome were subjected to secondary amplificationfocused on either the 5′- or 3′-boundary between genome and donor.Alignment of cloned fragments corresponding to these secondaryamplification products with the wild-type IPP2K genomic sequence as wellas the expected sequence of a targeted integration event clearlyindicated that the precise integration of donor DNA at the target siteoccurred.

Nucleotide sequence of the IPP2K genomic locus, the genome/donorboundary, nucleotide sequence of the donor regions corresponding toIPP2K homology flanks and nucleotide sequence of the herbicide tolerancecassette were all preserved in multiple cloned PCR products derived fromthis event. Therefore, this event represented a genome in whichhomology-driven repair of a ZFN-mediated double-stranded break andtargeted integration of a donor DNA at a specific gene target occurred.Additional transformed events representing unique targeted integrationoccurrences have been obtained, demonstrating that the methods taughtherein are reproducible in maize callus. One skilled in the art mightapply these methods to any gene target in any species of plant for whichtargeted integration is deemed desirable.

B. Nested Genome/Donor Specific Amplification

In this embodiment, both primary and subsequent secondary PCR reactionsutilized oligonucleotide primers specific for the regions of the IPP2Kgene target upstream or downstream of the donor integration region(appendices V and VI) in combination with oligonucleotide primersspecific for the donor sequence. In this example, primary PCRamplification reactions were carried out using reagents provided byTaKaRa Biotechnology Inc., Seta 3-4-1, Otsu, Shiga, 520-2193, Japan thatconsisted of the following: 2.5 μl 10× Ex Taq PCR™ Buffer, 40-200 ngdouble-stranded maize gDNA template, 10 μM forward oligonucleotide, 10μM reverse oligonucleotide primer, 2 μl dNTP mix (2.5 mM each), 16 μlH₂O, 0.5 μl (2.5 units) Ex Taq™ DNA polymerase. PCR reactions wereincubated using a Bio-Rad, 96-sample DNA Engine Tetrad2, Peltier ThermalCycler (Hercules, Calif.) under the following cycle conditions: 94° C.,3 min/1 cycle; 94° C. 3 sec, 52° C. or 64° C. 30 sec, 72° C. 2 min/35cycles; 72° C., 10 min/1 cycle; 4° C./hold.

The primary PCR reaction was then diluted 1:100 in H₂O and used astemplate DNA for a secondary PCR reaction. In this embodiment, thesecondary reactions also utilize primers that bind in the IPP2K genomicregion and the donor molecule, giving rise to an amplicon that spans theboundary of integration between genome and donor. The specific primersused determine whether the amplification is focused on either the 5′- or3′-boundary between genome and donor. Reagents for these reactionsconsisted of the following: 2.5 μl 10× Ex Taq PCR™ Buffer, 2 μl template[1:100 dilution of 1° PCR reaction], 10 μM forward oligonucleotideprimer, 10 μM reverse oligonucleotide primer, 2 μl dNTP mix (2.5 mMeach), 16 μl H₂O, 0.5 μl (2.5 units) Ex Taq™ DNA polymerase. PCRreactions were performed using a Bio-Rad, 96-sample DNA Engine Tetrad2,Peltier Thermal Cycler (Hercules, Calif.) under the following cycleconditions: 94° C., 3 min/1 cycle; 94° C. 30 sec, 54° C. or 60° C. 30sec, 72° C. 2 min/35 cycles; 72° C., 10 min/1 cycle; 4° C./hold. Twentyμl of each 2° PCR reaction was electrophoresed at 100 V for 1 hr in a1.0% TAE agarose gel supplemented with 0.5% ethidium bromide.

Amplified fragments were visualized with UV light and fragment sizeestimated by comparison with 1 Kbp Plus DNA ladder (Invitrogen LifeTechnologies, Carlsbad, Calif.). PCR products derived from targetedintegration of donor into the IPP2K gene were diagnosed by the presenceof DNA fragments 1.35 Kbp (5′-boundary) (FIG. 85) or 1.66 Kbp(3′-boundary) (FIG. 86). These fragments were gel-excised and purifiedaccording to manufacturer's directions using QIAquick Gel Extraction Kit(QIAGEN Inc., Valencia, Calif.). Purified fragments were subsequentlycloned into pCR2.1 plasmid using TOPO TA Cloning® Kit (with pCR® 2.1vector) and One Shot® TOP10 Chemically competent E. coli cells(Invitrogen Life Technologies, Carlsbad, Calif.) according tomanufacturer's protocol.

C. Nucleotide Sequence Analysis of Genotyping PCR Products

Individual colonies described in Example 21B were inoculated into a 14ml Falcon Tube (Becton-Dickinson, Franklin Lakes, N.J.) containing 2 mlTB supplemented with 50 μl/ml kanamycin and incubated for 16 hrs at 37°C. with shaking at 200 rpm. Following incubation, 1.5 ml cells weretransferred to a 1.7 ml Costar microcentrifuge tube (Fisher Scientific,Pittsburgh, Pa.) and pelleted at 16,000×g for 1 min. Supernatant wasremoved and plasmid DNA was isolated as described above usingNucleoSpin® Plasmid Kit (BD Biosciences/Clontech/Macherey-Nagel, PaloAlto, Calif.). Three μg of isolated plasmid was digested with 10 unitsEco RI (New England Biolabs, Beverly, Mass.). All plasmid digestionswere incubated for 1 hr at 37° C. Restricted DNA was electrophoresed at100 V for 1 hr in a 1.0% TAE agarose gel supplemented with 0.5% ethidiumbromide. Fragments were visualized with UV light and fragment sizeestimated by comparison with 1 Kbp Plus DNA ladder (Invitrogen LifeTechnologies, Carlsbad, Calif.).

Plasmid clones were diagnosed by the presence of inserted DNA fragmentsin addition to the 3.9 Kbp pCR® 2.1 vector. Double-stranded sequencingreactions of plasmid clones were performed as described by manufacturerusing CEQ™ DTCS-Quick Start Kit (Beckman-Coulter, Palo Alto, Calif.).Reactions were purified using Performa DTR Gel Filtration Cartridges(Edge BioSystems, Gaithersburg, Md.) as described by manufacturerprotocols. Sequence reactions were analyzed on a Beckman-Coulter CEQ™2000 XL DNA Analysis System and nucleotide characterization performedusing Sequencher™ version 4.1.4 (Gene Codes Corporation, Ann Arbor,Mich.). Nucleotide alignments were performed using Vector NTi version10.1 (Invitrogen Life Technologies, Carlsbad, Calif.).

Sequence data encompassing the boundary between upstream (5′-) IPP2Kgenomic sequence and donor DNA derived from multiple targetedintegration events was also obtained, including sequence dataencompassing the boundary between donor DNA and downstream (3′-) IPP2Kgenomic sequence derived from multiple targeted integration events aswell as sequence data including upstream (5′-) boundary sequencesderived from a single transformed callus event (#114). The transformedtargeted integration event (#114) was the result of integration of anautonomous donor into the IPP2K gene target.

In these analyses, both primary and secondary PCR amplificationreactions focused on either the 5′- or 3′-boundary between genome anddonor. Alignment of cloned fragments corresponding to these secondaryamplification products with the wild-type IPP2K genomic sequence as wellas the expected sequence of a targeted integration event revealed thatthe integration of donor DNA at the target site occurred. Nucleotidesequence of the IPP2K genomic locus, the genome/donor boundary,nucleotide sequence of the donor regions corresponding to IPP2K homologyflanks and nucleotide sequence of the herbicide tolerance cassette wereall preserved in multiple cloned PCR products derived from this event.

Therefore, this event represents a genome in which homology-drivenrepair of a ZFN-mediated double-stranded break at a specific gene targethas occurred. Additional transformed events representing unique targetedintegration occurrences have been obtained, demonstrating that themethods taught herein are reproducible in maize callus. One skilled inthe art might apply these methods to any gene target in any species ofplant for which targeted integration is deemed desirable.

Example 22 Regeneration of Fertile, Intact Plants from Maize CallusTissue

Isolated calli of herbicide-tolerant maize cells derived from HiII cellculture may be regenerated into intact, fertile maize plants. Oneskilled in the art might regenerate intact, fertile maize plants from avariety of embryogenic maize cell cultures.

In this example, regeneration of isolated, bialophos-resistant HiIIcalli was initiated by transferring isolated callus tissue to acytokinin-based induction medium, 28 (1H), containing MS salts andvitamins, 30.0 g/L sucrose, 5 mg/L benzylaminopurine, 0.25 mg/L 2,4-D, 1mg/L bialaphos, and 2.5 g/L Gelrite; pH 5.7. Cells were allowed to growin low light (13 μEm-2s-1) for one week followed by transfer toconditions of higher light (40 μEm-2s-1) for one week. Cells were thentransferred to regeneration medium, 36 (1H), which is identical to theinduction medium except that it lacks plant growth regulators. Small(3-5 cm) plantlets were excised with hand tools and placed into sterile150×25-mm glass culture tubes containing SHGA medium (Schenk andHildebrandt basal salts and vitamins, 1972, Can. J. Bot 50:199-204; 1g/L myo-inositol, 10 g/L sucrose, 2.0 g/L Gelrite, pH 5.8).

Once plantlets developed a sufficiently large and differentiated rootand shoot system, they were transplanted into 4-inch pots containingMetro-Mix 360 growing medium (Sun Gro Horticulture Canada Ltd.) andplaced in a greenhouse. The plantlets were fully or partially coveredwith clear plastic cups for 2-7 days, then transplanted to 5-gallon potscontaining a mixture consisting of 95% Metro-Mix 360 growing medium and5% clay/loam soil and grown to maturity. Plants may be self-pollinatedor cross-pollinated with an inbred line in order to produce T1 or F1seed, respectively. One skilled in the art might self-pollinateregenerated plants or cross pollinate regenerated plants with a varietyof germplasms in order to enable maize breeding.

Additional information related to targeted cleavage, targetedrecombination and targeted integration can be found in United StatesPatent Application publications US-2003-0232410; US-2005-0026157;US-2005-0064474; US-2005-0208489; and US-2006-0188987; and in U.S.patent application Ser. No. 11/493,423, filed Jul. 26, 2006, thedisclosures of which are incorporated by reference in their entiretiesfor all purposes.

All patents, patent applications and publications mentioned herein arehereby incorporated by reference, in their entireties, for all purposes.

Although disclosure has been provided in some detail by way ofillustration and example for the purposes of clarity of understanding,it will be apparent to those skilled in the art that various changes andmodifications can be practiced without departing from the spirit orscope of the disclosure. Accordingly, the foregoing descriptions andexamples should not be construed as limiting.

1. A zinc finger protein comprising a non-canonical (non-C₂H₂) zincfinger, wherein the non-canonical zinc finger has a helical portioninvolved in DNA binding and wherein the zinc-coordinating region of thehelical portion comprises the amino acid sequence HX₁X₂RCX_(L) (SEQ IDNO:2); and wherein the zinc finger protein is engineered to bind to atarget sequence.
 2. The zinc finger protein of claim 1, wherein X₁ is Aand X₂ is Q.
 3. The zinc finger protein of claim 1, wherein X₁ is K andX₂ is E.
 4. The zinc finger protein of claim 1, wherein X₁ is T and X₂is R.
 5. The zinc finger protein of claim 1, wherein X_(L) is G.
 6. Azinc finger protein of claim 1, wherein at least one zinc fingercomprises the sequenceCys-(X^(A))₂₋₄-Cys-(X^(B))₁₂-His-(X^(C))₃₋₅-Cys(X^(D))₁₋₁₀ (SEQ IDNO:3), where X^(A), X^(B), X^(C) and X^(D) can be any amino acid.
 7. Thezinc finger protein of claim 1, comprising any of the sequences shown inany of Tables 1, 2, 3 or
 4. 8. The zinc finger protein of claim 6,wherein X^(D) comprises the sequence QLV or QKP.
 9. The zinc fingerprotein of claim 8, wherein the sequence QLV or QKP are the 3 C-terminalamino acid residues of the zinc finger.
 10. The zinc finger protein ofclaim 6, wherein X^(D) comprises 1, 2 or 3 Gly (G) residues.
 11. A zincfinger protein comprising a plurality of zinc fingers, wherein at leastone of the zinc fingers comprises a CCHC zinc finger according toclaim
 1. 12. The zinc finger protein of claim 11, wherein the zincfinger protein comprises 3, 4, 5 or 6 zinc fingers.
 13. The zinc fingerprotein of claim 11, wherein finger 2 comprises the CCHC zinc finger.14. The zinc finger protein of claim 11, wherein the C-terminal zincfinger comprises the CCHC finger.
 15. The zinc finger protein of claim11, wherein at least two zinc fingers comprise the CCHC zinc finger. 16.The zinc finger protein of claim 11, wherein the zinc finger proteincomprises any of the sequences shown in Table 8 and is engineered tobind to a target sequence in an IPP2-K gene.
 17. A fusion proteincomprising a zinc finger protein of claim 1 and one or more functionaldomains.
 18. A fusion protein comprising: (a) a cleavage half-domain,(b) the zinc finger protein of claim 1, and (c) a ZC linker interposedbetween the cleavage half-domain and the zinc finger protein.
 19. Thefusion protein of claim 18, wherein the length of the ZC linker is 5amino acids.
 20. The fusion protein of claim 19, wherein the amino acidsequence of the ZC linker is GLRGS (SEQ ID NO:4).
 21. The fusion proteinof claim 18, wherein the length of the ZC linker is 6 amino acids. 22.The fusion protein of claim 21, wherein the amino acid sequence of theZC linker is GGLRGS (SEQ ID NO:5).
 23. A polynucleotide encoding a zincfinger protein according to claim
 1. 24. A method for targeted cleavageof cellular chromatin in a plant cell, the method comprising expressing,in the cell, a pair of fusion proteins according to claim 18; wherein:(a) the target sequences of the fusion proteins are within tennucleotides of each other; and (b) the fusion proteins dimerize andcleave DNA located between the target sequences.
 25. A method oftargeted genetic recombination in a host plant cell, the methodcomprising: (a) expressing, in the host cell, a pair of fusion proteinsaccording to claim 18, wherein the target sequences of the fusionproteins are present in a chosen host target locus; and (b) identifyinga recombinant host cell which exhibits a sequence alteration in the hosttarget locus.
 26. The method of claim 24, wherein the sequencealteration is a mutation selected from the group consisting of adeletion of genetic material, an insertion of genetic material, asubstitution of genetic material and any combination thereof.
 27. Themethod of claim 24, further comprising introducing an exogenouspolynucleotide into the host cell.
 28. The method of claim 27, whereinthe exogenous polynucleotide comprises sequences homologous to the hosttarget locus.
 29. The method of claim 24, wherein the plant is selectedfrom the group consisting of a monocotyledon, a dicotyledon, gymnospermsand eukaryotic algae.
 30. The method of claim 29, wherein the plant isselected from the group consisting of maize, rice, wheat, potato,soybean, tomato, tobacco, members of the Brassica family, andArabidopsis.
 31. The method of claim 24, wherein the plant is a tree.32. The method of claim 24, wherein the target sequences are in an IPP2Kgene.
 33. A method for reducing the level of phytic acid in seeds, themethod comprising inactivating or altering an IPP2-K gene according toclaim
 32. 34. A method for making phosphorous more metabolicallyavailable in seed, the method comprising inactivating or altering anIPP2-K gene according to claim
 32. 35. A plant cell comprising a zincfinger protein according to claim
 1. 36. The plant cell of claim 35,wherein the cell is a seed.
 37. The plant cell of claim 36, wherein seedis a corn seed.
 38. The plant cell of claim 35, wherein IPP2-K ispartially or fully inactivated.
 39. The plant cell of claim 38, whereinthe levels of phytic acid in the seed are reduced.
 40. The plant cell ofclaim 35, wherein metabolically available levels of phosphorous in thecell are increased.